Variant report

Variant	rs2071507
Chromosome Location	chr3:52826707-52826708
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:67)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:67 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr3:52826456-52826811	K562	blood:	n/a	n/a
2	CTCF	chr3:52826584-52826716	MCF-7	breast:	n/a	n/a
3	CTCF	chr3:52826537-52826762	K562	blood:	n/a	n/a
4	CTCF	chr3:52826560-52826710	HepG2	liver:	n/a	n/a
5	CTCF	chr3:52826660-52826810	HFF-Myc	foreskin:	n/a	n/a
6	CTCF	chr3:52826560-52826710	WERI-Rb-1	eye:	n/a	n/a
7	CTCF	chr3:52826445-52826783	H1-hESC	embryonic stem cell:	n/a	n/a
8	RAD21	chr3:52826481-52826789	H1-hESC	embryonic stem cell:	n/a	chr3:52826649-52826663
9	CTCF	chr3:52826680-52826830	BJ	skin:	n/a	n/a
10	CTCF	chr3:52826421-52826858	H1-hESC	embryonic stem cell:	n/a	n/a
11	CTCF	chr3:52826580-52826730	HepG2	liver:	n/a	n/a
12	CTCF	chr3:52826580-52826730	GM12865	blood:	n/a	n/a
13	CUX1	chr3:52826455-52826720	K562	blood:	n/a	n/a
14	CTCF	chr3:52826534-52826770	H1-hESC	embryonic stem cell:	n/a	n/a
15	CTCF	chr3:52826580-52826730	GM12866	blood:	n/a	n/a
16	CTCF	chr3:52826583-52826723	MCF-7	breast:	n/a	n/a
17	CTCF	chr3:52826560-52826850	SAEC	small airway:	n/a	n/a
18	CTCF	chr3:52826580-52826730	HA-sp	spinal cord:	n/a	n/a
19	CTCF	chr3:52826600-52826750	WERI-Rb-1	eye:	n/a	n/a
20	CTCF	chr3:52826560-52826710	HEK293	kidney:	n/a	n/a
21	CTCF	chr3:52826560-52826710	HPAF	blood vessel:	n/a	n/a
22	CTCF	chr3:52826700-52826850	HAc	cerebellar:	n/a	n/a
23	ZNF143	chr3:52826484-52826827	H1-hESC	embryonic stem cell:	n/a	n/a
24	NFIC	chr3:52826422-52826754	HepG2	liver:	n/a	n/a
25	GABPA	chr3:52826506-52826822	H1-hESC	embryonic stem cell:	n/a	n/a
26	CTCF	chr3:52826577-52826716	MCF-7	breast:	n/a	n/a
27	FOXA1	chr3:52826316-52826770	HepG2	liver:	n/a	n/a
28	CTCF	chr3:52826600-52826750	Hela-S3	cervix:	n/a	n/a
29	CTCF	chr3:52826560-52826710	AG04449	skin:	n/a	n/a
30	CTCF	chr3:52826560-52826710	GM06990	blood:	n/a	n/a
31	RAD21	chr3:52826436-52826814	HepG2	liver:	n/a	chr3:52826649-52826663
32	RAD21	chr3:52826429-52826877	HepG2	liver:	n/a	chr3:52826649-52826663
33	CTCF	chr3:52826600-52826750	HFF-Myc	foreskin:	n/a	n/a
34	CTCF	chr3:52826560-52826710	HCM	heart:	n/a	n/a
35	CTCF	chr3:52826580-52826730	HCM	heart:	n/a	n/a
36	RAD21	chr3:52826414-52826763	HepG2	liver:	n/a	chr3:52826649-52826663
37	CTCF	chr3:52826554-52826741	Hela-S3	cervix:	n/a	n/a
38	CTCF	chr3:52826490-52826748	HepG2	liver:	n/a	n/a
39	FOXA1	chr3:52826379-52826839	HepG2	liver:	n/a	n/a
40	RAD21	chr3:52826474-52826787	H1-hESC	embryonic stem cell:	n/a	chr3:52826649-52826663
41	CTCF	chr3:52826560-52826710	Caco-2	colon:	n/a	n/a
42	MAFK	chr3:52826549-52826712	HepG2	liver:	n/a	n/a
43	RAD21	chr3:52826535-52826716	K562	blood:	n/a	chr3:52826649-52826663
44	CTCF	chr3:52826415-52826846	K562	blood:	n/a	n/a
45	RAD21	chr3:52826532-52826707	K562	blood:	n/a	chr3:52826649-52826663
46	CTCF	chr3:52826580-52826730	GM12872	blood:	n/a	n/a
47	CTCF	chr3:52826554-52826758	K562	blood:	n/a	n/a
48	ZBTB7A	chr3:52826562-52826724	HepG2	liver:	n/a	n/a
49	CTCF	chr3:52826560-52826710	K562	blood:	n/a	n/a
50	CTCF	chr3:52826560-52826710	GM12873	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52818572..52822409-chr3:52823256..52828567,5	K562	blood:

No data

Variant related genes	Relation type
ITIH3	TF binding region
ENSG00000055957	Chromatin interaction

Extended variants
information (count: 122 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:115)

rs_ID	r²[population]
rs1014969	0.91[JPT][hapmap]
rs1029871	0.91[JPT][hapmap];0.82[EUR][1000 genomes]
rs1042779	0.81[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10510760	0.91[JPT][hapmap]
rs1075653	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1076425	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10780035	0.91[JPT][hapmap]
rs10865973	0.91[JPT][hapmap]
rs10865974	0.91[JPT][hapmap]
rs1108842	0.83[JPT][hapmap]
rs11130310	0.86[JPT][hapmap]
rs11130312	0.91[JPT][hapmap]
rs11130315	0.91[JPT][hapmap]
rs11130317	0.91[JPT][hapmap]
rs11130323	0.91[JPT][hapmap]
rs11130327	0.82[EUR][1000 genomes]
rs11177	0.86[JPT][hapmap]
rs11714419	0.91[JPT][hapmap]
rs11716747	0.91[JPT][hapmap]
rs11717836	0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12487591	0.91[JPT][hapmap]
rs12488461	0.90[JPT][hapmap]
rs12496634	0.91[JPT][hapmap]
rs12497998	0.91[JPT][hapmap]
rs12635140	0.91[JPT][hapmap]
rs13061423	0.81[EUR][1000 genomes]
rs13064064	0.91[JPT][hapmap]
rs13068293	0.91[JPT][hapmap]
rs13071584	0.91[JPT][hapmap]
rs13079063	0.95[JPT][hapmap]
rs13082208	0.95[JPT][hapmap]
rs13082960	0.91[JPT][hapmap]
rs13083798	0.86[JPT][hapmap]
rs13085775	0.83[JPT][hapmap]
rs13085895	0.91[JPT][hapmap]
rs13095332	0.81[EUR][1000 genomes]
rs1561337	0.91[JPT][hapmap]
rs1866268	0.91[JPT][hapmap]
rs2019065	0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2028216	0.91[JPT][hapmap]
rs2071506	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2071508	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2072390	0.91[JPT][hapmap]
rs2079929	0.91[JPT][hapmap]
rs2083180	0.91[JPT][hapmap]
rs2118540	0.86[JPT][hapmap]
rs2159644	0.91[JPT][hapmap]
rs2164884	0.95[JPT][hapmap]
rs2164885	0.95[JPT][hapmap]
rs2230534	0.83[EUR][1000 genomes]
rs2230535	0.91[JPT][hapmap];0.83[EUR][1000 genomes]
rs2239549	0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2239550	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2239551	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2239699	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2240919	1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2240920	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2268023	0.84[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2268024	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2268025	0.92[JPT][hapmap];0.82[EUR][1000 genomes]
rs2268026	0.91[JPT][hapmap]
rs2268027	0.91[JPT][hapmap]
rs2270197	1.00[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2284350	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2284351	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2286798	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2289247	0.91[JPT][hapmap]
rs2289250	0.91[JPT][hapmap]
rs2300149	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2302417	0.83[ASN][1000 genomes]
rs2336149	0.91[JPT][hapmap]
rs2336545	0.91[JPT][hapmap]
rs2535629	0.91[CHB][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2577831	0.83[JPT][hapmap]
rs2710323	0.87[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs2710331	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs33967311	0.91[JPT][hapmap]
rs34017441	0.95[JPT][hapmap]
rs35526119	0.91[JPT][hapmap]
rs3617	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs3733039	0.91[JPT][hapmap]
rs3733041	0.91[JPT][hapmap]
rs3733045	0.91[JPT][hapmap]
rs3755798	0.91[JPT][hapmap]
rs3755806	0.91[JPT][hapmap]
rs3774354	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3774355	0.82[CEU][hapmap];0.96[CHB][hapmap];0.92[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3774365	0.91[JPT][hapmap]
rs3774366	0.91[JPT][hapmap]
rs4687548	0.91[JPT][hapmap]
rs4687550	1.00[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap]
rs4687551	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4687552	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4687638	0.91[JPT][hapmap]
rs4687650	0.84[EUR][1000 genomes]
rs4687654	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6445534	0.87[JPT][hapmap]
rs6445535	0.91[JPT][hapmap]
rs6617	0.91[JPT][hapmap]
rs6762813	0.91[JPT][hapmap]
rs6778329	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs678	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6792369	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6804145	0.91[JPT][hapmap]
rs6976	0.91[JPT][hapmap]
rs736408	0.83[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs746694	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7611731	0.91[JPT][hapmap]
rs7622694	0.91[JPT][hapmap]
rs7624716	0.91[JPT][hapmap]
rs767418	0.90[JPT][hapmap]
rs8906	0.91[JPT][hapmap]
rs9324	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9881468	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs998909	0.95[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv984563	chr3:52516115-52867075	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv834698	chr3:52749983-52928219	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
3	esv2762328	chr3:52774884-53002150	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	esv3446915	chr3:52786850-53049217	Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv1010761	chr3:52804547-52851258	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	esv1810629	chr3:52817031-52869635	Weak transcription Active TSS Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv876797	chr3:52817675-52873984	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs2071507	PBRM1	cis	Thyroid	GTEx
rs2071507	FLJ12442	cis	multi-tissue	Pritchard
rs2071507	NT5DC2	cis	multi-tissue	Pritchard
rs2071507	NT5DC2	cis	Skin Sun Exposed Lower leg	GTEx
rs2071507	ITIH3	cis	multi-tissue	Pritchard
rs2071507	NT5DC2	cis	Lymphoblastoid	GTEx
rs2071507	ITIH4-AS1	cis	Artery Tibial	GTEx
rs2071507	MUSTN1	cis	Artery Aorta	GTEx
rs2071507	NT5DC2	Cis_1M	lymphoblastoid	RTeQTL
rs2071507	GLT8D1	Cis_1M	lymphoblastoid	RTeQTL
rs2071507	ITIH4-AS1	cis	Artery Aorta	GTEx

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52823600-52827000	Weak transcription	Spleen	Spleen
2	chr3:52824000-52832800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:52825400-52827800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
4	chr3:52825800-52836200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:52826000-52826800	Enhancers	Fetal Intestine Small	intestine
6	chr3:52826000-52829000	Enhancers	Fetal Muscle Leg	muscle
7	chr3:52826200-52826800	Enhancers	Fetal Intestine Large	intestine
8	chr3:52826200-52827400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr3:52826400-52828200	Enhancers	Liver	Liver
10	chr3:52826600-52827600	Enhancers	HepG2	liver
11	chr3:52826600-52828800	Weak transcription	Pancreas	Pancrea

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