Variant report

Variant	rs10865971
Chromosome Location	chr3:52481406-52481407
allele	A/G
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	CTCF	chr3:52481046-52481428	GM12878	blood:	n/a	chr3:52481218-52481226 chr3:52481214-52481230 chr3:52481213-52481231 chr3:52481208-52481229
2	RAD21	chr3:52480991-52481472	ECC-1	luminal epithelium:	n/a	chr3:52481142-52481156 chr3:52481211-52481230 chr3:52481221-52481228
3	RUNX3	chr3:52480896-52481437	GM12878	blood:	n/a	n/a
4	YY1	chr3:52480917-52481411	HepG2	liver:	n/a	n/a
5	RFX5	chr3:52481121-52481424	GM12878	blood:	n/a	n/a
6	RAD21	chr3:52480683-52481777	SK-N-SH	brain:	n/a	chr3:52481571-52481584 chr3:52481579-52481588 chr3:52480862-52480875 chr3:52481573-52481592 chr3:52481142-52481156 chr3:52481576-52481589 chr3:52481211-52481230 chr3:52481221-52481228 chr3:52480932-52480946
7	CTCF	chr3:52480660-52481486	HCT-116	colon:	n/a	chr3:52481218-52481226 chr3:52480858-52480867 chr3:52481214-52481230 chr3:52480933-52480942 chr3:52480861-52480874 chr3:52481213-52481231 chr3:52481208-52481229
8	NRF1	chr3:52481155-52481438	GM12878	blood:	n/a	n/a
9	ZNF143	chr3:52481037-52481577	GM12878	blood:	n/a	n/a
10	RAD21	chr3:52480954-52481474	A549	lung:	n/a	chr3:52481142-52481156 chr3:52481211-52481230 chr3:52481221-52481228
11	TBL1XR1	chr3:52481105-52481448	GM12878	blood:	n/a	n/a
12	RCOR1	chr3:52481047-52481492	K562	blood:	n/a	n/a
13	RAD21	chr3:52481044-52481408	K562	blood:	n/a	chr3:52481142-52481156 chr3:52481211-52481230 chr3:52481221-52481228
14	CTCF	chr3:52480994-52481484	IMR90	lung:	n/a	chr3:52481218-52481226 chr3:52481214-52481230 chr3:52481213-52481231 chr3:52481208-52481229
15	CTCF	chr3:52481004-52481488	K562	blood:	n/a	chr3:52481218-52481226 chr3:52481214-52481230 chr3:52481213-52481231 chr3:52481208-52481229
16	MAFK	chr3:52481081-52481455	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr3:52480785-52481683	ECC-1	luminal epithelium:	n/a	n/a
18	CTCF	chr3:52480995-52481480	GM12878	blood:	n/a	chr3:52481218-52481226 chr3:52481214-52481230 chr3:52481213-52481231 chr3:52481208-52481229
19	CTCF	chr3:52481087-52481411	Hela-S3	cervix:	n/a	chr3:52481218-52481226 chr3:52481214-52481230 chr3:52481213-52481231 chr3:52481208-52481229
20	CHD2	chr3:52481384-52481431	HepG2	liver:	n/a	n/a
21	WRNIP1	chr3:52481099-52481507	GM12878	blood:	n/a	n/a
22	RAD21	chr3:52480897-52481511	HepG2	liver:	n/a	chr3:52481142-52481156 chr3:52481211-52481230 chr3:52481221-52481228 chr3:52480932-52480946
23	RAD21	chr3:52480978-52481476	H1-hESC	embryonic stem cell:	n/a	chr3:52481142-52481156 chr3:52481211-52481230 chr3:52481221-52481228
24	CTCF	chr3:52480983-52481426	ECC-1	luminal epithelium:	n/a	chr3:52481218-52481226 chr3:52481214-52481230 chr3:52481213-52481231 chr3:52481208-52481229
25	CTCF	chr3:52481300-52481450	A549	lung:	n/a	n/a
26	FOXM1	chr3:52480998-52481442	GM12878	blood:	n/a	n/a
27	CTCF	chr3:52481086-52481409	K562	blood:	n/a	chr3:52481218-52481226 chr3:52481214-52481230 chr3:52481213-52481231 chr3:52481208-52481229
28	MAFK	chr3:52481125-52481407	HepG2	liver:	n/a	n/a
29	MAFK	chr3:52481085-52481424	IMR90	lung:	n/a	n/a
30	MAFK	chr3:52481135-52481435	Hela-S3	cervix:	n/a	n/a
31	ZNF143	chr3:52481037-52481566	K562	blood:	n/a	n/a
32	CTCF	chr3:52481055-52481412	Lung_OC	lung:	n/a	chr3:52481218-52481226 chr3:52481214-52481230 chr3:52481213-52481231 chr3:52481208-52481229
33	RCOR1	chr3:52481138-52481452	Hela-S3	cervix:	n/a	n/a
34	SIN3A	chr3:52481073-52481442	H1-hESC	embryonic stem cell:	n/a	n/a
35	SMC3	chr3:52481003-52481410	HepG2	liver:	n/a	chr3:52481215-52481229
36	MXI1	chr3:52480836-52481531	SK-N-SH	brain:	n/a	n/a
37	CTCF	chr3:52480961-52481506	H1-hESC	embryonic stem cell:	n/a	chr3:52481218-52481226 chr3:52481214-52481230 chr3:52481213-52481231 chr3:52481208-52481229
38	RFX5	chr3:52481137-52481471	H1-hESC	embryonic stem cell:	n/a	n/a
39	MAZ	chr3:52481048-52481627	IMR90	lung:	n/a	n/a
40	RAD21	chr3:52480851-52481532	A549	lung:	n/a	chr3:52480862-52480875 chr3:52481142-52481156 chr3:52481211-52481230 chr3:52481221-52481228 chr3:52480932-52480946
41	RAD21	chr3:52480999-52481478	H1-hESC	embryonic stem cell:	n/a	chr3:52481142-52481156 chr3:52481211-52481230 chr3:52481221-52481228
42	BACH1	chr3:52481078-52481608	H1-hESC	embryonic stem cell:	n/a	n/a
43	SMC3	chr3:52480998-52481429	Hela-S3	cervix:	n/a	chr3:52481215-52481229
44	CTCF	chr3:52480956-52481486	H1-hESC	embryonic stem cell:	n/a	chr3:52481218-52481226 chr3:52481214-52481230 chr3:52481213-52481231 chr3:52481208-52481229
45	RAD21	chr3:52480865-52481553	H1-hESC	embryonic stem cell:	n/a	chr3:52481142-52481156 chr3:52481211-52481230 chr3:52481221-52481228 chr3:52480932-52480946
46	STAT5A	chr3:52481024-52481583	GM12878	blood:	n/a	n/a
47	CTCF	chr3:52481007-52481431	K562	blood:	n/a	chr3:52481218-52481226 chr3:52481214-52481230 chr3:52481213-52481231 chr3:52481208-52481229
48	JUND	chr3:52481100-52481443	H1-hESC	embryonic stem cell:	n/a	n/a
49	RAD21	chr3:52481018-52481408	A549	lung:	n/a	chr3:52481142-52481156 chr3:52481211-52481230 chr3:52481221-52481228
50	BHLHE40	chr3:52481197-52481413	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:52462455..52463343-chr3:52480708..52481906,6	MCF-7	breast:
2	chr3:52444714..52445234-chr3:52480809..52481724,2	K562	blood:
3	chr3:52456149..52459336-chr3:52479539..52482914,3	MCF-7	breast:
4	chr3:52462408..52463664-chr3:52480773..52481689,4	K562	blood:
5	chr3:52324567..52326107-chr3:52479756..52482200,2	K562	blood:
6	chr3:52479566..52481452-chr3:52488469..52490137,2	K562	blood:
7	chr3:52445926..52446427-chr3:52480871..52481709,2	MCF-7	breast:
8	chr3:52476521..52480604-chr3:52481219..52484302,3	MCF-7	breast:
9	chr3:52462441..52466581-chr3:52481054..52483159,4	K562	blood:
10	chr3:52446194..52446753-chr3:52480736..52481697,3	K562	blood:
11	chr3:52461011..52465347-chr3:52480548..52485332,5	MCF-7	breast:
12	chr3:52445252..52447300-chr3:52479403..52482047,3	MCF-7	breast:
13	chr3:52462259..52463205-chr3:52480718..52481619,5	MCF-7	breast:
14	chr3:52443376..52445165-chr3:52479554..52482269,2	K562	blood:

Variant related genes	Relation type
SEMA3G	TF binding region
ENSG00000168237	Chromatin interaction
ENSG00000010322	Chromatin interaction
ENSG00000010318	Chromatin interaction
ENSG00000010319	Chromatin interaction
ENSG00000163930	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10460962	1.00[CEU][hapmap];0.88[GIH][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs10461027	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs10461028	0.80[EUR][1000 genomes]
rs11706515	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs11707056	1.00[CEU][hapmap];0.88[GIH][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs11708581	0.91[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs11708811	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11710014	1.00[CEU][hapmap];0.88[GIH][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs11711974	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs11713914	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs11714358	0.83[EUR][1000 genomes]
rs11715208	0.83[EUR][1000 genomes]
rs11716487	1.00[CEU][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes]
rs11717028	0.85[EUR][1000 genomes]
rs11720365	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11721277	0.88[EUR][1000 genomes]
rs17052051	1.00[CEU][hapmap]
rs17052052	1.00[CEU][hapmap];0.88[GIH][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs17052053	0.91[CEU][hapmap];0.91[TSI][hapmap]
rs17052054	1.00[CEU][hapmap];0.88[GIH][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs17263770	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1767	0.91[CEU][hapmap]
rs1769	1.00[CEU][hapmap];0.88[GIH][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs35976326	0.83[EUR][1000 genomes]
rs3733063	0.91[CEU][hapmap];0.91[TSI][hapmap]
rs3886875	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs55676974	0.83[EUR][1000 genomes]
rs55806905	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55813842	0.88[EUR][1000 genomes]
rs56002041	0.88[EUR][1000 genomes]
rs56322342	0.88[EUR][1000 genomes]
rs56899118	0.88[EUR][1000 genomes]
rs57849650	0.88[EUR][1000 genomes]
rs61644644	0.83[EUR][1000 genomes]
rs6445385	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs6776759	0.92[EUR][1000 genomes]
rs6783652	0.83[EUR][1000 genomes]
rs6793317	0.91[CEU][hapmap];0.91[TSI][hapmap]
rs724801	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs729555	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73072990	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73088791	0.83[EUR][1000 genomes]
rs73091166	0.88[EUR][1000 genomes]
rs73091168	0.88[EUR][1000 genomes]
rs746239	0.88[EUR][1000 genomes]
rs7615405	0.85[EUR][1000 genomes]
rs7633687	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7643913	0.86[CEU][hapmap];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	nsv984542	chr3:52285682-52516115	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	94 gene(s)	inside rSNPs	diseases
3	nsv834697	chr3:52400578-52579417	Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv876792	chr3:52430526-52575831	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv876793	chr3:52450043-52584787	Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	esv1818902	chr3:52481406-52572056	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs10865971	LOC286359	trans	parietal	SCAN
rs10865971	DNAH1	cis	parietal	SCAN
rs10865971	DNAH1	cis	cerebellum	SCAN
rs10865971	NISCH	cis	parietal	SCAN
rs10865971	PPM1M	cis	Artery Tibial	GTEx
rs10865971	SEMA3G	cis	cerebellum	SCAN
rs10865971	NISCH	cis	lymphoblastoid	seeQTL

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52470800-52484200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:52478200-52484000	Enhancers	Fetal Heart	heart
3	chr3:52478800-52487600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr3:52479200-52481800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
5	chr3:52479200-52483800	Weak transcription	HMEC	breast
6	chr3:52479400-52481600	Enhancers	Skeletal Muscle Female	skeletal muscle
7	chr3:52479400-52483000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr3:52479400-52483000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr3:52479400-52483800	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr3:52479400-52483800	Weak transcription	Liver	Liver
11	chr3:52479400-52483800	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr3:52479400-52483800	Weak transcription	A549	lung
13	chr3:52479400-52484000	Weak transcription	Esophagus	oesophagus
14	chr3:52479400-52484000	Weak transcription	Fetal Intestine Large	intestine
15	chr3:52479400-52484200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr3:52479400-52484200	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr3:52479400-52485200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:52479400-52487200	Weak transcription	GM12878-XiMat	blood
19	chr3:52479400-52488200	Weak transcription	Colonic Mucosa	Colon
20	chr3:52479600-52483800	Weak transcription	Gastric	stomach
21	chr3:52479600-52483800	Weak transcription	Pancreas	Pancrea
22	chr3:52479600-52483800	Weak transcription	Hela-S3	cervix
23	chr3:52479600-52484000	Weak transcription	Spleen	Spleen
24	chr3:52479600-52487000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr3:52479600-52487400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr3:52479600-52487600	Weak transcription	Duodenum Mucosa	Duodenum
27	chr3:52479600-52487600	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr3:52479600-52487800	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr3:52479800-52482800	Weak transcription	HSMMtube	muscle
30	chr3:52479800-52483800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr3:52480400-52481600	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr3:52480400-52481600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
33	chr3:52480600-52482000	Enhancers	Fetal Muscle Leg	muscle
34	chr3:52480800-52481600	Enhancers	HUES48 Cell Line	embryonic stem cell
35	chr3:52480800-52481600	Enhancers	Primary T cells fromperipheralblood	blood
36	chr3:52480800-52481600	Enhancers	Placenta	Placenta
37	chr3:52480800-52483000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
38	chr3:52481000-52481600	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr3:52481000-52481600	Enhancers	Stomach Mucosa	stomach
40	chr3:52481000-52483800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr3:52481000-52483800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr3:52481200-52481600	Enhancers	ES-I3 Cell Line	embryonic stem cell
43	chr3:52481200-52482600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr3:52481200-52482800	Weak transcription	Lung	lung
45	chr3:52481200-52483800	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr3:52481200-52483800	Weak transcription	Right Ventricle	heart
47	chr3:52481200-52484200	Weak transcription	Left Ventricle	heart
48	chr3:52481200-52484200	Enhancers	HepG2	liver
49	chr3:52481200-52484600	Weak transcription	Right Atrium	heart
50	chr3:52481200-52487600	Weak transcription	Stomach Smooth Muscle	stomach

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