Variant report

Variant	rs3846059
Chromosome Location	chr3:42695313-42695314
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	NFIC	chr3:42693953-42695609	SK-N-SH	brain:	n/a	chr3:42694172-42694188 chr3:42694172-42694189
2	POLR2A	chr3:42693885-42695434	U87	brain:	n/a	n/a
3	POLR2A	chr3:42693977-42695668	K562	blood:	n/a	n/a
4	MXI1	chr3:42695214-42695474	Hela-S3	cervix:	n/a	n/a
5	EP300	chr3:42694012-42695401	ECC-1	luminal epithelium:	n/a	chr3:42694489-42694505 chr3:42694545-42694561
6	ZBTB7A	chr3:42694819-42697395	ECC-1	luminal epithelium:	n/a	chr3:42697295-42697303
7	JUND	chr3:42692900-42695764	SK-N-SH	brain:	n/a	chr3:42693498-42693510 chr3:42693230-42693240 chr3:42693230-42693240 chr3:42693230-42693240 chr3:42693229-42693241 chr3:42693500-42693508 chr3:42693230-42693240 chr3:42693499-42693510
8	POLR2A	chr3:42694026-42695756	HUVEC	blood vessel:	n/a	n/a
9	NFIC	chr3:42693913-42695654	ECC-1	luminal epithelium:	n/a	chr3:42694172-42694188 chr3:42694172-42694189
10	POLR2A	chr3:42693838-42695371	U87	brain:	n/a	n/a
11	POLR2A	chr3:42694988-42695375	HCT-116	colon:	n/a	n/a
12	NFIC	chr3:42693950-42695598	ECC-1	luminal epithelium:	n/a	chr3:42694172-42694188 chr3:42694172-42694189
13	ZBTB7A	chr3:42694008-42695723	ECC-1	luminal epithelium:	n/a	n/a
14	MAZ	chr3:42695120-42695401	HepG2	liver:	n/a	n/a
15	TCF12	chr3:42692854-42695443	SK-N-SH	brain:	n/a	chr3:42694507-42694514 chr3:42694856-42694865
16	POLR2A	chr3:42694102-42696721	HUVEC	blood vessel:	n/a	n/a
17	POLR2A	chr3:42693850-42695747	U87	brain:	n/a	n/a
18	TCF12	chr3:42694130-42697494	ECC-1	luminal epithelium:	n/a	chr3:42694507-42694514 chr3:42697092-42697099 chr3:42694856-42694865
19	POLR2A	chr3:42695018-42695336	ECC-1	luminal epithelium:	n/a	n/a
20	MAX	chr3:42695284-42696849	HepG2	liver:	n/a	chr3:42696527-42696537 chr3:42696528-42696537 chr3:42696528-42696537 chr3:42696530-42696539 chr3:42696528-42696537 chr3:42696527-42696538 chr3:42696527-42696538 chr3:42696528-42696538
21	SMC3	chr3:42695151-42695344	Hela-S3	cervix:	n/a	n/a
22	MYC	chr3:42695194-42696751	K562	blood:	n/a	chr3:42696527-42696537 chr3:42696528-42696537 chr3:42696528-42696537 chr3:42696530-42696539 chr3:42696528-42696537 chr3:42696527-42696538 chr3:42696527-42696538 chr3:42696528-42696538
23	POLR2A	chr3:42695205-42695467	HepG2	liver:	n/a	n/a
24	MAZ	chr3:42692512-42697572	IMR90	lung:	n/a	chr3:42696527-42696537 chr3:42696528-42696537 chr3:42697183-42697193 chr3:42693401-42693411 chr3:42696528-42696537 chr3:42696530-42696539 chr3:42696528-42696537 chr3:42696527-42696538 chr3:42696527-42696538 chr3:42696528-42696538
25	MAX	chr3:42695134-42697012	A549	lung:	n/a	chr3:42696527-42696537 chr3:42696528-42696537 chr3:42696528-42696537 chr3:42696530-42696539 chr3:42696528-42696537 chr3:42696527-42696538 chr3:42696527-42696538 chr3:42696528-42696538
26	POLR2A	chr3:42694172-42695629	ProgFib	skin:	n/a	n/a
27	SMARCC1	chr3:42694093-42695556	Hela-S3	cervix:	n/a	n/a
28	MAX	chr3:42694952-42696806	HepG2	liver:	n/a	chr3:42696527-42696537 chr3:42696528-42696537 chr3:42696528-42696537 chr3:42696530-42696539 chr3:42696528-42696537 chr3:42696527-42696538 chr3:42696527-42696538 chr3:42696528-42696538
29	CTCF	chr3:42695200-42695350	HUVEC	blood vessel:	n/a	n/a
30	MTA3	chr3:42695226-42695605	GM12878	blood:	n/a	n/a
31	JUN	chr3:42693670-42695594	K562	blood:	n/a	n/a
32	RCOR1	chr3:42695213-42695733	K562	blood:	n/a	n/a
33	MAZ	chr3:42695120-42696781	Hela-S3	cervix:	n/a	chr3:42696527-42696537 chr3:42696528-42696537 chr3:42696528-42696537 chr3:42696530-42696539 chr3:42696528-42696537 chr3:42696527-42696538 chr3:42696527-42696538 chr3:42696528-42696538
34	BHLHE40	chr3:42695243-42695981	K562	blood:	n/a	n/a
35	POLR2A	chr3:42694935-42695359	SK-N-SH	brain:	n/a	n/a
36	MAX	chr3:42694994-42696079	ECC-1	luminal epithelium:	n/a	n/a
37	POLR2A	chr3:42695144-42695427	Hela-S3	cervix:	n/a	n/a
38	HMGN3	chr3:42694965-42696679	K562	blood:	n/a	n/a
39	MAX	chr3:42694740-42696735	Hela-S3	cervix:	n/a	chr3:42696527-42696537 chr3:42696528-42696537 chr3:42696528-42696537 chr3:42696530-42696539 chr3:42696528-42696537 chr3:42696527-42696538 chr3:42696527-42696538 chr3:42696528-42696538
40	MXI1	chr3:42692903-42697530	SK-N-SH	brain:	n/a	chr3:42696527-42696536 chr3:42696527-42696536 chr3:42694036-42694045 chr3:42696529-42696538
41	MXI1	chr3:42692869-42697394	IMR90	lung:	n/a	chr3:42696527-42696536 chr3:42696527-42696536 chr3:42694036-42694045 chr3:42696529-42696538
42	ZBTB7A	chr3:42695100-42696614	K562	blood:	n/a	n/a
43	POLR2A	chr3:42694887-42695403	HUVEC	blood vessel:	n/a	n/a
44	MAX	chr3:42695125-42696889	K562	blood:	n/a	chr3:42696527-42696537 chr3:42696528-42696537 chr3:42696528-42696537 chr3:42696530-42696539 chr3:42696528-42696537 chr3:42696527-42696538 chr3:42696527-42696538 chr3:42696528-42696538
45	POLR2A	chr3:42695272-42695323	H1-hESC	embryonic stem cell:	n/a	n/a
46	ELF1	chr3:42694930-42696670	GM12878	blood:	n/a	chr3:42695919-42695931 chr3:42696029-42696038 chr3:42695623-42695636

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:42695307-42695357	Jurkat	blood:	n/a
2	chr3:42695307-42695357	HRPEpiC	eye:	n/a
3	chr3:42695307-42695357	SK-N-SH	brain:	n/a
4	chr3:42695307-42695357	HUVEC	blood vessel:	n/a
5	chr3:42695307-42695357	AG04449	skin:	fetal
6	chr3:42695307-42695357	BE2_C	brain:	n/a
7	chr3:42695307-42695357	NHDF-neo	bronchial:	n/a
8	chr3:42695307-42695357	HepG2	liver:	n/a
9	chr3:42695307-42695357	AG09319	gingival:	n/a
10	chr3:42695307-42695357	PrEC	prostate:	n/a
11	chr3:42695307-42695357	SKMC	muscle:	n/a
12	chr3:42695307-42695357	HCM	heart:	n/a
13	chr3:42695307-42695357	A549	lung:	n/a
14	chr3:42695307-42695357	HEK293	kidney:	embryo
15	chr3:42695307-42695357	HL-60	blood:	n/a
16	chr3:42695307-42695357	GM12891	blood:	n/a
17	chr3:42695307-42695357	NHBE	bronchial:	n/a
18	chr3:42695307-42695357	SK-N-SH_RA	brain:	n/a
19	chr3:42695307-42695357	ovcar-3	ovarian:	n/a
20	chr3:42695307-42695357	GM12892	blood:	n/a
21	chr3:42695307-42695357	RPTEC	kidney:	n/a
22	chr3:42695307-42695357	HPAEpiC	pulmonary alveolar:	n/a
23	chr3:42695307-42695357	LNCaP	prostate:	n/a
24	chr3:42695307-42695357	GM19239	blood:	n/a
25	chr3:42695307-42695357	PANC-1	pancreas:	n/a
26	chr3:42695307-42695357	HNPCEpiC	eye:	n/a
27	chr3:42695307-42695357	HCF	heart:	n/a
28	chr3:42695307-42695357	SAEC	small airway:	n/a
29	chr3:42695307-42695357	AG09309	skin:	n/a
30	chr3:42695307-42695357	MCF10A-Er-Src	breast:	n/a
31	chr3:42695307-42695357	H1-hESC	embryonic stem cell:	embryo
32	chr3:42695307-42695357	HRCEpiC	kidney:	n/a
33	chr3:42695307-42695357	K562	blood:	n/a
34	chr3:42695307-42695357	ECC-1	luminal epithelium:	n/a
35	chr3:42695307-42695357	ProgFib	skin:	n/a
36	chr3:42695307-42695357	BJ	skin:	n/a
37	chr3:42695307-42695357	HCPEpiC	choroid plexus:	n/a
38	chr3:42695307-42695357	SK-N-MC	brain:	n/a
39	chr3:42695307-42695357	NB4	blood:	n/a
40	chr3:42695307-42695357	CMK	blood:	n/a
41	chr3:42695307-42695357	MCF-7	breast:	n/a
42	chr3:42695307-42695357	AG10803	skin:	n/a
43	chr3:42695307-42695357	GM06990	blood:	n/a
44	chr3:42695307-42695357	IMR90	lung:	fetal
45	chr3:42695307-42695357	Hela-S3	cervix:	n/a
46	chr3:42695307-42695357	HMEC	breast:	n/a
47	chr3:42695307-42695357	HEEpiC	esophagus:	n/a
48	chr3:42695307-42695357	T-47D	breast:	n/a
49	chr3:42695307-42695357	AG04450	lung:	fetal
50	chr3:42695307-42695357	PFSK-1	brain:	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:42632553..42639930-chr3:42692933..42696882,8	K562	blood:
2	chr3:42659807..42662376-chr3:42694804..42697042,2	MCF-7	breast:
3	chr3:42620456..42625490-chr3:42691753..42697487,7	K562	blood:
4	chr3:42640678..42643591-chr3:42694568..42696079,2	K562	blood:
5	chr3:42640361..42643591-chr3:42693270..42696162,5	K562	blood:
6	chr3:42631026..42632613-chr3:42695067..42697159,2	MCF-7	breast:

Variant related genes	Relation type
ZBTB47	TF binding region
ZBTB47	CpG island
ENSG00000093183	Chromatin interaction
ENSG00000114857	Chromatin interaction
ENSG00000008324	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs1062051	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13067987	0.81[EUR][1000 genomes]
rs13072295	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13085695	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13089845	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13090902	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13093680	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.82[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13095447	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17074602	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs17074662	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.97[LWK][hapmap];0.82[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17074664	1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs17074669	1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs17074673	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17074674	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17074680	1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs17074693	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2241542	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs2284303	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2284304	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2300057	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.82[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2300058	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2302352	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.82[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33969824	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs33984028	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34683820	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34687113	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34762478	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34801786	1.00[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34852409	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34977988	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35216140	0.82[EUR][1000 genomes]
rs35506005	0.82[ASN][1000 genomes]
rs35676838	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35770315	0.89[ASN][1000 genomes]
rs35871059	0.82[EUR][1000 genomes]
rs35890296	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36033201	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36043081	0.82[EUR][1000 genomes]
rs3774401	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3774402	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3774404	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3774406	0.82[ASN][1000 genomes]
rs3774407	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3821836	1.00[CHB][hapmap];0.89[CHD][hapmap];0.88[JPT][hapmap]
rs3846058	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3856737	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3886782	0.82[ASN][1000 genomes]
rs3900780	0.81[EUR][1000 genomes]
rs56047094	0.82[EUR][1000 genomes]
rs56797870	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57259216	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58868911	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59914338	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60232916	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60348477	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60535002	0.82[EUR][1000 genomes]
rs61149998	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6441928	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66786953	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67059259	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67165547	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67533173	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67583158	0.82[EUR][1000 genomes]
rs6771105	0.82[EUR][1000 genomes]
rs6772312	0.81[ASN][1000 genomes]
rs6778982	1.00[CEU][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6782164	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67832425	0.82[EUR][1000 genomes]
rs6788548	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6790204	0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs6793186	1.00[CEU][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6795296	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6797491	0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs68004576	0.82[EUR][1000 genomes]
rs68028490	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs68071013	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72864072	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73829255	0.82[EUR][1000 genomes]
rs7616701	0.85[TSI][hapmap]
rs7617403	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7617736	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7623867	0.81[EUR][1000 genomes]
rs7624628	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002944	chr3:42559762-42728909	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	esv1818302	chr3:42688867-42709062	Active TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv876731	chr3:42690285-42711655	Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3846059	C3orf39	cis	parietal	SCAN
rs3846059	HHATL	cis	cerebellum	SCAN
rs3846059	CCR1	cis	cerebellum	SCAN
rs3846059	SNORA62	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42692600-42695400	Flanking Active TSS	Osteobl	bone
2	chr3:42692600-42695600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
3	chr3:42692600-42695600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
4	chr3:42692800-42695400	Flanking Active TSS	Rectal Smooth Muscle	rectum
5	chr3:42692800-42695400	Flanking Active TSS	Stomach Smooth Muscle	stomach
6	chr3:42692800-42695400	Flanking Active TSS	HSMMtube	muscle
7	chr3:42693000-42695400	Flanking Active TSS	HSMM	muscle
8	chr3:42693000-42695600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr3:42693200-42695400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
10	chr3:42693200-42695400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr3:42693200-42695400	Flanking Active TSS	Right Ventricle	heart
12	chr3:42693200-42695400	Flanking Active TSS	A549	lung
13	chr3:42693200-42695400	Flanking Active TSS	Hela-S3	cervix
14	chr3:42693400-42695600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
15	chr3:42693600-42695400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr3:42693600-42695600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:42693600-42695600	Flanking Active TSS	Adipose Nuclei	Adipose
18	chr3:42693600-42695600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
19	chr3:42693600-42695600	Flanking Active TSS	HMEC	breast
20	chr3:42693800-42695400	Flanking Active TSS	HUVEC	blood vessel
21	chr3:42693800-42695400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
22	chr3:42693800-42695600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
23	chr3:42693800-42695600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
24	chr3:42693800-42695600	Flanking Active TSS	Duodenum Mucosa	Duodenum
25	chr3:42693800-42695600	Flanking Active TSS	GM12878-XiMat	blood
26	chr3:42693800-42695600	Flanking Active TSS	NH-A	brain
27	chr3:42694000-42695400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr3:42694000-42695400	Flanking Active TSS	NHEK	skin
29	chr3:42694000-42695600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
30	chr3:42694000-42695600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr3:42694000-42695600	Flanking Active TSS	Colonic Mucosa	Colon
32	chr3:42694000-42695600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
33	chr3:42694000-42696800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr3:42694200-42695400	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr3:42694200-42695400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
36	chr3:42694200-42695600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr3:42694200-42695600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr3:42694200-42695600	Flanking Active TSS	Fetal Muscle Trunk	muscle
39	chr3:42694200-42695600	Flanking Active TSS	Fetal Muscle Leg	muscle
40	chr3:42694200-42695600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
41	chr3:42694200-42695600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
42	chr3:42694200-42695800	Enhancers	Fetal Brain Male	brain
43	chr3:42694400-42695400	Enhancers	Primary T helper naive cells from peripheral blood	blood
44	chr3:42694400-42695600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
45	chr3:42694400-42695600	Flanking Active TSS	Stomach Mucosa	stomach
46	chr3:42694400-42695600	Flanking Active TSS	K562	blood
47	chr3:42694400-42695800	Flanking Active TSS	Primary B cells from cord blood	blood
48	chr3:42694400-42695800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
49	chr3:42694400-42697000	Active TSS	Aorta	Aorta
50	chr3:42694600-42695400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast

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