Variant report

Variant	rs1888488
Chromosome Location	chr21:40686521-40686522
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr21:40685288-40687099	SK-N-MC	brain:	n/a	n/a
2	E2F6	chr21:40685284-40686675	H1-hESC	embryonic stem cell:	n/a	chr21:40685427-40685439 chr21:40685548-40685557 chr21:40685550-40685560
3	POLR2A	chr21:40684951-40686864	ProgFib	skin:	n/a	n/a
4	POLR2A	chr21:40685298-40686961	GM12878	blood:	n/a	n/a
5	POLR2A	chr21:40684903-40686876	K562	blood:	n/a	n/a
6	POLR2A	chr21:40685164-40686821	ECC-1	luminal epithelium:	n/a	n/a
7	POLR2A	chr21:40685074-40686979	K562	blood:	n/a	n/a
8	RCOR1	chr21:40686356-40686672	K562	blood:	n/a	n/a
9	UBTF	chr21:40684951-40686805	K562	blood:	n/a	n/a
10	POLR2A	chr21:40685320-40686932	K562	blood:	n/a	n/a
11	POU2F2	chr21:40685309-40686892	GM12878	blood:	n/a	chr21:40685864-40685876 chr21:40685768-40685780 chr21:40685867-40685879
12	TBP	chr21:40685371-40686719	H1-hESC	embryonic stem cell:	n/a	n/a
13	RELA	chr21:40685304-40686773	GM15510	blood:	n/a	n/a
14	E2F4	chr21:40685026-40686759	K562	blood:	n/a	chr21:40685109-40685119 chr21:40685427-40685439 chr21:40685548-40685557 chr21:40685141-40685151 chr21:40685550-40685560 chr21:40685111-40685120
15	PML	chr21:40685283-40686737	MCF-7	breast:	n/a	n/a
16	RCOR1	chr21:40685534-40686585	GM12878	blood:	n/a	n/a
17	ZNF143	chr21:40685459-40686713	H1-hESC	embryonic stem cell:	n/a	chr21:40685866-40685884
18	RAD21	chr21:40685703-40686698	IMR90	lung:	n/a	chr21:40685853-40685867 chr21:40685855-40685868
19	CCNT2	chr21:40684902-40686697	K562	blood:	n/a	chr21:40685051-40685060 chr21:40685265-40685274 chr21:40685765-40685774
20	EBF1	chr21:40686503-40686764	GM12878	blood:	n/a	n/a
21	POLR2A	chr21:40685154-40686915	HL-60	blood:	n/a	n/a
22	POLR2A	chr21:40685252-40686938	GM12891	blood:	n/a	n/a
23	SIN3AK20	chr21:40684015-40687111	MCF-7	breast:	n/a	n/a
24	POLR2A	chr21:40684347-40686942	K562	blood:	n/a	n/a
25	POLR2A	chr21:40684890-40687595	K562	blood:	n/a	n/a
26	CHD2	chr21:40685403-40686780	H1-hESC	embryonic stem cell:	n/a	chr21:40685430-40685440 chr21:40685423-40685433
27	HEY1	chr21:40684916-40686853	K562	blood:	n/a	chr21:40685861-40685876 chr21:40685748-40685763 chr21:40685144-40685159 chr21:40685469-40685484
28	POLR2A	chr21:40685056-40686987	K562	blood:	n/a	n/a
29	FOS	chr21:40686478-40686637	MCF10A-Er-Src	breast:	n/a	n/a
30	TBP	chr21:40685300-40686865	K562	blood:	n/a	n/a
31	MAZ	chr21:40685080-40686679	Hela-S3	cervix:	n/a	chr21:40685337-40685347 chr21:40685086-40685096
32	POLR2A	chr21:40684964-40686717	GM18526	blood:	n/a	n/a
33	REST	chr21:40683818-40686869	H1-neurons	neurons:	n/a	chr21:40685323-40685336
34	POLR2A	chr21:40685117-40686938	K562	blood:	n/a	n/a
35	POLR2A	chr21:40685534-40686781	U87	brain:	n/a	n/a
36	TEAD4	chr21:40684911-40686578	SK-N-SH	brain:	n/a	n/a
37	POLR2A	chr21:40685105-40687059	GM12892	blood:	n/a	n/a
38	ELF1	chr21:40685342-40686767	K562	blood:	n/a	chr21:40685830-40685839 chr21:40685876-40685885
39	POLR2A	chr21:40684380-40686835	Hela-S3	cervix:	n/a	n/a
40	POLR2A	chr21:40684324-40686793	GM12892	blood:	n/a	n/a
41	POLR2A	chr21:40685306-40686804	GM12878	blood:	n/a	n/a
42	POLR2A	chr21:40685286-40686822	H1-hESC	embryonic stem cell:	n/a	n/a
43	CTCF	chr21:40686480-40686630	K562	blood:	n/a	n/a
44	CREB1	chr21:40685239-40686659	HepG2	liver:	n/a	n/a
45	MAX	chr21:40685148-40686851	ECC-1	luminal epithelium:	n/a	chr21:40685337-40685347
46	JUND	chr21:40685300-40686894	K562	blood:	n/a	chr21:40685433-40685442 chr21:40685426-40685435
47	POLR2A	chr21:40684267-40686937	GM18505	blood:	n/a	n/a
48	HCFC1	chr21:40685317-40686777	K562	blood:	n/a	n/a
49	POLR2A	chr21:40685303-40686688	IMR90	lung:	n/a	n/a
50	MAX	chr21:40685133-40686805	A549	lung:	n/a	chr21:40685337-40685347

No.	Distal block	Cell Line	Cell type
1	chr21:40683319..40690926-chr21:40755872..40762716,23	MCF-7	breast:
2	chr2:238392237..238394703-chr21:40685639..40687456,2	MCF-7	breast:
3	chr21:40554013..40557423-chr21:40684520..40688084,3	MCF-7	breast:
4	chr21:40685228..40687774-chr21:40751832..40753804,3	K562	blood:
5	chr11:64545391..64546081-chr21:40685867..40686815,2	NB4	blood:
6	chr21:40681596..40696529-chr21:40715399..40724266,46	K562	blood:
7	21:40686083-40686932..21:40748850-40752541	K562	blood:
8	21:40686083-40686932..21:40757151-40764378	K562	blood:
9	chr21:40683837..40687545-chr21:40816624..40819639,6	K562	blood:
10	chr21:40681416..40687854-chr21:40744378..40751195,8	K562	blood:
11	chr21:40683876..40687631-chr21:40749667..40753921,6	K562	blood:
12	chr21:40685837..40686745-chr5:175875260..175875880,2	Hela-S3	cervix:
13	chr21:40683271..40692626-chr21:40743960..40754349,22	MCF-7	breast:
14	chr21:40684466..40689800-chr21:40758261..40763098,10	K562	blood:
15	chr21:40683646..40687466-chr21:40813293..40816602,5	MCF-7	breast:
16	chr21:40686237..40688163-chr21:40821826..40824303,2	MCF-7	breast:
17	chr21:40682856..40693378-chr21:40754350..40765471,56	MCF-7	breast:
18	chr21:40683489..40689074-chr21:40750757..40754639,9	MCF-7	breast:
19	chr21:40685845..40686781-chr3:9438942..9439442,2	Hela-S3	cervix:
20	chr21:40684332..40690368-chr21:40756970..40764337,16	K562	blood:
21	chr21:40684444..40687629-chr3:63848425..63851169,6	MCF-7	breast:
22	chr21:40684582..40688018-chr21:40762846..40766549,4	MCF-7	breast:
23	chr21:40553454..40557456-chr21:40682892..40687176,12	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-BRWD1-IT2-1	chr21:40685861-40686888	NONHSAT082161
2	lnc-BRWD1-IT2-1	chr21:40685887-40686886	ENSG00000255568.2

Variant related genes	Relation type
BRWD1-IT2	TF binding region
BRWD1	TF binding region
BRWD1-AS1	TF binding region
ENSG00000227406	Chromatin interaction
ENSG00000113194	Chromatin interaction
ENSG00000252915	Chromatin interaction
ENSG00000185437	Chromatin interaction
ENSG00000183527	Chromatin interaction
ENSG00000163634	Chromatin interaction
ENSG00000182093	Chromatin interaction
ENSG00000168137	Chromatin interaction
ENSG00000163635	Chromatin interaction
ENSG00000115648	Chromatin interaction
ENSG00000168066	Chromatin interaction
ENSG00000205581	Chromatin interaction
ENSG00000206573	Chromatin interaction
ENSG00000272991	Chromatin interaction
ENSG00000157578	Chromatin interaction
ENSG00000238556	Chromatin interaction

Extended variants
information (count: 149 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:141)

rs_ID	r²[population]
rs1011413	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10154217	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1041439	0.84[CHB][hapmap]
rs11088471	1.00[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11088472	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11910705	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11910906	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11910971	0.84[CHB][hapmap]
rs11911822	0.92[CEU][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12482181	0.92[ASW][hapmap];0.86[YRI][hapmap]
rs12626405	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13051430	0.84[CHB][hapmap]
rs13625	0.92[ASW][hapmap];0.86[YRI][hapmap]
rs14194	0.92[ASW][hapmap];0.86[YRI][hapmap]
rs1541100	0.84[CHB][hapmap]
rs1541102	0.92[ASW][hapmap];0.86[YRI][hapmap]
rs1882779	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1888487	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1963676	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1984022	0.86[YRI][hapmap]
rs1984748	0.84[CHB][hapmap]
rs2005933	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2026265	0.86[YRI][hapmap]
rs2026266	0.84[CHB][hapmap]
rs2037925	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2142111	0.88[CEU][hapmap];0.87[JPT][hapmap];0.85[YRI][hapmap];0.82[AMR][1000 genomes]
rs2142117	0.84[CHB][hapmap]
rs2150410	0.84[CHB][hapmap]
rs2150413	0.92[ASW][hapmap];0.96[YRI][hapmap]
rs2150414	0.92[ASW][hapmap];0.96[YRI][hapmap]
rs2150415	0.92[ASW][hapmap];0.84[YRI][hapmap]
rs2183573	0.88[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes]
rs2183575	0.83[CHB][hapmap]
rs2183576	0.83[CHB][hapmap]
rs2234543	0.92[ASW][hapmap];0.86[YRI][hapmap]
rs2245455	1.00[ASW][hapmap];0.89[CEU][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap];0.81[LWK][hapmap];0.81[TSI][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes]
rs2272576	0.95[CHB][hapmap];0.83[ASN][1000 genomes]
rs2272577	0.95[CHB][hapmap];0.81[CHD][hapmap];0.85[ASN][1000 genomes]
rs2272578	0.85[ASN][1000 genomes]
rs2297258	0.84[ASN][1000 genomes]
rs2410104	0.84[CHB][hapmap]
rs2410123	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2410124	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2735306	0.83[MEX][hapmap]
rs2836925	0.92[ASW][hapmap];0.86[YRI][hapmap]
rs2836929	0.92[ASW][hapmap];0.86[YRI][hapmap]
rs2836932	0.92[ASW][hapmap];0.86[YRI][hapmap]
rs2836933	0.86[YRI][hapmap]
rs2836956	0.92[ASW][hapmap];0.96[YRI][hapmap]
rs2836957	0.86[YRI][hapmap]
rs2836958	0.92[ASW][hapmap];0.96[YRI][hapmap]
rs2836964	0.92[ASW][hapmap];0.86[YRI][hapmap]
rs2836965	0.92[ASW][hapmap];0.86[YRI][hapmap]
rs2836967	0.86[YRI][hapmap]
rs2836968	0.92[ASW][hapmap];0.86[YRI][hapmap]
rs2836969	0.88[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2836971	0.88[CHB][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2836974	0.92[ASW][hapmap];0.86[YRI][hapmap]
rs2836975	0.92[CEU][hapmap];0.84[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2836981	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.94[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2836982	1.00[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.94[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2836985	0.92[ASW][hapmap]
rs2836986	0.96[CEU][hapmap];0.89[YRI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2836987	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2836988	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34240248	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34436313	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35182074	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35909862	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs371625	0.84[AMR][1000 genomes]
rs3746885	0.84[ASN][1000 genomes]
rs3746886	0.84[ASN][1000 genomes]
rs377098	0.88[CEU][hapmap];0.87[JPT][hapmap];0.84[AMR][1000 genomes]
rs414850	0.82[AMR][1000 genomes]
rs418298	0.89[CEU][hapmap];0.91[GIH][hapmap];0.87[JPT][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes]
rs418359	0.88[CEU][hapmap];0.91[GIH][hapmap];0.87[JPT][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes]
rs419469	0.85[ASW][hapmap];0.89[CEU][hapmap];0.91[GIH][hapmap];0.87[JPT][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes]
rs428602	0.88[CEU][hapmap];0.87[JPT][hapmap];0.96[YRI][hapmap];0.83[AMR][1000 genomes]
rs429955	0.82[AMR][1000 genomes]
rs442972	0.84[AMR][1000 genomes]
rs452377	0.84[AMR][1000 genomes]
rs4624474	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4816619	0.84[CHB][hapmap]
rs4816620	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4816623	0.86[ASN][1000 genomes]
rs4817999	0.82[AMR][1000 genomes]
rs4818005	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4818007	0.84[CHB][hapmap]
rs4818011	0.84[CHB][hapmap]
rs4818015	0.92[CEU][hapmap];0.89[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4818017	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61300849	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6517519	0.92[ASW][hapmap];0.86[YRI][hapmap]
rs6517523	0.92[ASW][hapmap];0.86[YRI][hapmap]
rs6517526	0.92[ASW][hapmap];0.86[YRI][hapmap]
rs6517529	0.84[CHB][hapmap]
rs6517531	0.83[CHB][hapmap]
rs6517532	0.84[CHB][hapmap]
rs6517535	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6517538	0.92[ASW][hapmap];0.86[YRI][hapmap]
rs6517540	0.85[ASN][1000 genomes]
rs6517541	0.95[CHB][hapmap];0.81[CHD][hapmap];0.85[ASN][1000 genomes]
rs718225	0.84[CHB][hapmap]
rs719230	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7275773	0.84[CHB][hapmap]
rs7276774	0.86[CEU][hapmap];0.88[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7278297	0.96[YRI][hapmap]
rs7278985	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7279558	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7280326	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7280375	0.92[ASW][hapmap];0.86[YRI][hapmap]
rs7281853	1.00[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.94[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7282604	0.89[CEU][hapmap];0.91[GIH][hapmap];0.87[JPT][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes]
rs7283439	0.84[CHB][hapmap]
rs7283516	0.86[YRI][hapmap]
rs8127087	0.86[YRI][hapmap]
rs8127391	0.84[CHB][hapmap]
rs8127986	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8128026	0.83[YRI][hapmap]
rs8128102	0.82[YRI][hapmap]
rs8128118	0.86[CHB][hapmap]
rs8130795	0.84[AMR][1000 genomes]
rs8130854	0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8130984	0.88[YRI][hapmap]
rs8131150	0.84[CHB][hapmap]
rs8131263	0.84[CHB][hapmap]
rs8132230	0.84[CHB][hapmap]
rs8132285	0.86[YRI][hapmap]
rs9636957	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs973521	0.84[CHB][hapmap]
rs997147	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9974757	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9975119	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9975562	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9975614	0.80[ASN][1000 genomes]
rs9978591	0.84[CHB][hapmap]
rs9978775	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9979483	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9981301	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9981656	0.86[ASN][1000 genomes]
rs9982111	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv459259	chr21:40571246-40701169	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv587480	chr21:40571246-40701169	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	esv3429298	chr21:40670131-40688774	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	nsv913744	chr21:40670167-40757973	Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
5	esv3439649	chr21:40683507-40687455	Genic enhancers Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
6	nsv1059420	chr21:40684295-40745952	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
7	nsv587482	chr21:40684427-40706594	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
8	nsv587483	chr21:40686327-40718161	Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs1888488	BRWD1	cis	Cerebellum	GTEx
rs1888488	BRWD1	cis	lymphoblastoid	seeQTL
rs1888488	BRWD1	cis	cerebellum	SCAN
rs1888488	PSMG1	cis	Artery Tibial	GTEx
rs1888488	PSMG1	cis	Esophagus Mucosa	GTEx
rs1888488	BRWD1	cis	Frontal Cortex	GTEx
rs1888488	PSMG1	cis	lung	GTEx
rs1888488	BRWD1	Cis_1M	lymphoblastoid	RTeQTL
rs1888488	BRWD1	cis	Temporal Cortex	GTEx
rs1888488	PSMG1	cis	Skin Sun Exposed Lower leg	GTEx
rs1888488	PSMG1	cis	lymphoblastoid	seeQTL
rs1888488	PSMG1	cis	parietal	SCAN
rs1888488	BRWD1	cis	parietal	SCAN
rs1888488	BRWD1	cis	Brain Pons	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40683600-40686600	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr21:40684000-40686600	Active TSS	H1 Cell Line	embryonic stem cell
3	chr21:40684000-40686600	Active TSS	Aorta	Aorta
4	chr21:40684000-40686600	Active TSS	Sigmoid Colon	Sigmoid Colon
5	chr21:40684200-40686600	Active TSS	H9 Cell Line	embryonic stem cell
6	chr21:40684200-40686600	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr21:40684200-40686600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr21:40684200-40686600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr21:40684200-40686600	Active TSS	Duodenum Smooth Muscle	Duodenum
10	chr21:40684200-40686600	Active TSS	Fetal Intestine Large	intestine
11	chr21:40684200-40686600	Active TSS	Fetal Intestine Small	intestine
12	chr21:40684200-40686600	Active TSS	Fetal Stomach	stomach
13	chr21:40684200-40686600	Active TSS	Left Ventricle	heart
14	chr21:40684200-40686600	Active TSS	Ovary	ovary
15	chr21:40684200-40686600	Active TSS	Psoas Muscle	Psoas
16	chr21:40684200-40686600	Active TSS	Stomach Smooth Muscle	stomach
17	chr21:40684200-40686600	Active TSS	HSMM	muscle
18	chr21:40684200-40686800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
19	chr21:40684200-40686800	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr21:40684400-40686600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr21:40684400-40686600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr21:40684400-40686600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr21:40684400-40686600	Active TSS	HUES64 Cell Line	embryonic stem cell
24	chr21:40684400-40686600	Active TSS	iPS-20b Cell Line	embryonic stem cell
25	chr21:40684400-40686600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr21:40684400-40686600	Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr21:40684400-40686600	Active TSS	Colon Smooth Muscle	Colon
28	chr21:40684400-40686600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
29	chr21:40684400-40686600	Active TSS	Gastric	stomach
30	chr21:40684400-40686600	Active TSS	Lung	lung
31	chr21:40684400-40686600	Active TSS	Rectal Smooth Muscle	rectum
32	chr21:40684400-40686600	Active TSS	Spleen	Spleen
33	chr21:40684400-40686600	Active TSS	NHLF	lung
34	chr21:40684400-40686800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr21:40684400-40686800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr21:40684400-40686800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr21:40684400-40686800	Active TSS	Colonic Mucosa	Colon
38	chr21:40684400-40687000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr21:40684400-40687000	Active TSS	A549	lung
40	chr21:40684600-40686600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr21:40685600-40686600	Active TSS	Stomach Mucosa	stomach
42	chr21:40686000-40686600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
43	chr21:40686000-40686600	Bivalent/Poised TSS	HepG2	liver
44	chr21:40686000-40686800	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr21:40686000-40686800	Flanking Active TSS	Primary hematopoietic stem cells	blood
46	chr21:40686000-40686800	Flanking Active TSS	Placenta Amnion	Placenta Amnion
47	chr21:40686000-40686800	Flanking Active TSS	HUVEC	blood vessel
48	chr21:40686000-40687000	Flanking Active TSS	Primary B cells from cord blood	blood
49	chr21:40686000-40687000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
50	chr21:40686000-40687000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin

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