Variant report

Variant	rs2092698
Chromosome Location	chr1:94316410-94316411
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:178)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:178 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:94316320-94316470	HBMEC	blood vessel:	n/a	n/a
2	PAX5	chr1:94316056-94316564	GM12878	blood:	n/a	n/a
3	REST	chr1:94316198-94316506	H1-hESC	embryonic stem cell:	n/a	n/a
4	MAX	chr1:94316188-94316517	K562	blood:	n/a	n/a
5	CTCF	chr1:94316325-94316616	Gliobla	brain:	n/a	n/a
6	CTCF	chr1:94316193-94316810	K562	blood:	n/a	n/a
7	CTCF	chr1:94316320-94316470	HCT-116	colon:	n/a	n/a
8	RFX5	chr1:94316269-94316607	Hela-S3	cervix:	n/a	n/a
9	CTCF	chr1:94316320-94316470	HL-60	blood:	n/a	n/a
10	CTCF	chr1:94316320-94316470	GM12866	blood:	n/a	n/a
11	CTCF	chr1:94316320-94316470	AG10803	skin:	n/a	n/a
12	CTCF	chr1:94316280-94316629	K562	blood:	n/a	n/a
13	CTCF	chr1:94316340-94316490	BE2_C	brain:	n/a	n/a
14	CTCF	chr1:94316320-94316470	NHEK	skin:	n/a	n/a
15	RAD21	chr1:94316196-94316662	H1-hESC	embryonic stem cell:	n/a	n/a
16	CTCF	chr1:94316295-94316606	K562	blood:	n/a	n/a
17	CTCF	chr1:94316404-94316578	GM10266	blood:	n/a	n/a
18	CTCF	chr1:94316381-94316610	GM12878	blood:	n/a	n/a
19	CTCF	chr1:94316320-94316470	GM12864	blood:	n/a	n/a
20	CTCF	chr1:94316340-94316490	NHLF	lung:	n/a	n/a
21	CBX3	chr1:94316156-94316636	K562	blood:	n/a	n/a
22	CTCF	chr1:94316360-94316510	GM12867	blood:	n/a	n/a
23	CTCF	chr1:94316320-94316470	HPAF	blood vessel:	n/a	n/a
24	RAD21	chr1:94316281-94316641	Hela-S3	cervix:	n/a	n/a
25	CTCF	chr1:94316300-94316450	A549	lung:	n/a	n/a
26	CTCF	chr1:94316320-94316470	HPF	lung:	n/a	n/a
27	CTCF	chr1:94316342-94316588	NHEK	skin:	n/a	n/a
28	CTCF	chr1:94316384-94316566	GM19239	blood:	n/a	n/a
29	CTCF	chr1:94316320-94316470	HAc	cerebellar:	n/a	n/a
30	CTCF	chr1:94316363-94316517	T-47D	breast:	n/a	n/a
31	CTCF	chr1:94316320-94316470	NB4	blood:	n/a	n/a
32	CTCF	chr1:94316409-94316588	Lung_OC	lung:	n/a	n/a
33	CTCF	chr1:94316381-94316595	ProgFib	skin:	n/a	n/a
34	CTCF	chr1:94316320-94316470	HRE	kidney:	n/a	n/a
35	CTCF	chr1:94316294-94316602	H1-hESC	embryonic stem cell:	n/a	n/a
36	CTCF	chr1:94316360-94316510	GM12870	blood:	n/a	n/a
37	CTCF	chr1:94316340-94316490	AG04450	lung:	n/a	n/a
38	CTCF	chr1:94316406-94316554	MCF-7	breast:	n/a	n/a
39	CTCF	chr1:94316300-94316450	HFF-Myc	foreskin:	n/a	n/a
40	WRNIP1	chr1:94316280-94316467	GM12878	blood:	n/a	n/a
41	CTCF	chr1:94316320-94316470	HMF	breast:	n/a	n/a
42	SETDB1	chr1:94315987-94316632	U2OS	brain:	n/a	n/a
43	CTCF	chr1:94316278-94316654	GM12878	blood:	n/a	n/a
44	CTCF	chr1:94316398-94316587	GM10248	blood:	n/a	n/a
45	CTCF	chr1:94316300-94316450	GM12869	blood:	n/a	n/a
46	CTCF	chr1:94316244-94316618	A549	lung:	n/a	n/a
47	REST	chr1:94316268-94316487	MCF-7	breast:	n/a	n/a
48	CTCF	chr1:94316392-94316560	MCF-7	breast:	n/a	n/a
49	CTCF	chr1:94316320-94316470	HUVEC	blood vessel:	n/a	n/a
50	CTCF	chr1:94316180-94316470	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:94311804..94314669-chr1:94314970..94317163,2	MCF-7	breast:
2	chr1:94315633..94319063-chr1:94342848..94345734,4	K562	blood:
3	chr1:94085637..94087323-chr1:94315969..94317684,2	MCF-7	breast:
4	chr1:94309833..94313487-chr1:94314841..94317688,5	K562	blood:
5	chr1:94307315..94310834-chr1:94315340..94316960,3	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FNBP1L-2	chr1:94312708-94317158	NONHSAT004550

No data

Variant related genes	Relation type
BCAR3	TF binding region
ENSG00000067334	Chromatin interaction
ENSG00000260464	Chromatin interaction
ENSG00000211575	Chromatin interaction
ENSG00000137936	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1051394	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11165021	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11165022	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11165023	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11165025	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11165026	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12023010	0.94[AFR][1000 genomes]
rs12029548	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12029637	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12029670	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12041975	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12097812	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12758972	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1884019	0.80[EUR][1000 genomes]
rs2092699	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2103784	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2143992	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2273165	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2273166	0.86[ASN][1000 genomes]
rs2391315	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2391321	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3789459	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3789460	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4847191	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4847192	0.80[EUR][1000 genomes]
rs4847193	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4847263	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4847264	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6664876	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6666633	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6667991	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6681169	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6681265	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6684054	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6697189	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7364663	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7367601	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7513489	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7513786	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7514828	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7517632	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7518940	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7523787	0.80[EUR][1000 genomes]
rs7555136	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7556047	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7556107	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1822452	chr1:94278128-94320233	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	121 gene(s)	inside rSNPs	diseases
2	nsv998755	chr1:94294015-94341712	Flanking Active TSS Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	121 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2092698	RP11-488P3.1	cis	lung	GTEx
rs2092698	RP11-488P3.1	cis	Skin Sun Exposed Lower leg	GTEx
rs2092698	RP11-488P3.1	cis	Muscle Skeletal	GTEx
rs2092698	DNTTIP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94314200-94317000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr1:94314200-94332800	Weak transcription	Brain Cingulate Gyrus	brain
3	chr1:94314200-94334200	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr1:94314200-94334400	Weak transcription	Brain Substantia Nigra	brain
5	chr1:94315600-94316800	Enhancers	Primary T cells fromperipheralblood	blood
6	chr1:94316000-94317200	Enhancers	Skeletal Muscle Female	skeletal muscle
7	chr1:94316200-94316800	Enhancers	K562	blood
8	chr1:94316400-94316800	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr1:94316400-94318200	Weak transcription	Hela-S3	cervix

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