Variant report

Variant	rs11922961
Chromosome Location	chr3:52868610-52868611
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	chr3:52868594-52868818	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52867798..52869834-chr3:52876401..52878497,2	MCF-7	breast:

Variant related genes	Relation type
ITIH4	TF binding region
ENSG00000243696	TF binding region
ENSG00000248592	Chromatin interaction
ENSG00000213533	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10865977	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11130331	0.87[CEU][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap]
rs11715347	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11719137	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11915546	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11918800	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11922975	0.92[CEU][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap]
rs12487379	0.89[EUR][1000 genomes]
rs12492391	0.96[CEU][hapmap];0.86[CHB][hapmap]
rs12638968	0.81[EUR][1000 genomes]
rs13072536	0.83[CHB][hapmap]
rs13072537	0.89[EUR][1000 genomes]
rs13083728	0.83[CHB][hapmap];0.82[CHD][hapmap]
rs1573815	0.83[CHB][hapmap];0.82[CHD][hapmap]
rs2071042	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs2239547	0.86[CHB][hapmap];0.82[CHD][hapmap]
rs2239548	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2240915	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2240917	0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2245538	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2245647	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2256332	0.87[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.91[TSI][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2276817	0.83[CHB][hapmap];0.82[CHD][hapmap]
rs2276823	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2276825	0.83[CHB][hapmap];0.82[CHD][hapmap]
rs2336558	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2336664	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2336667	0.81[EUR][1000 genomes]
rs2336668	0.96[CEU][hapmap];0.91[CHB][hapmap];0.81[EUR][1000 genomes]
rs2535627	0.90[YRI][hapmap]
rs2535633	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3733047	0.83[CHB][hapmap];0.82[CHD][hapmap]
rs3774364	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3821873	0.96[CEU][hapmap];0.86[CHB][hapmap]
rs4350911	0.83[EUR][1000 genomes]
rs4687554	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs4687657	0.83[CHB][hapmap];0.80[CHD][hapmap]
rs4687658	0.87[CHB][hapmap]
rs4687663	0.83[CHB][hapmap]
rs4687672	0.83[CHB][hapmap]
rs4687680	0.96[CEU][hapmap];0.86[CHB][hapmap]
rs4687682	0.96[CEU][hapmap];0.91[CHB][hapmap];0.82[AMR][1000 genomes]
rs4687683	0.81[EUR][1000 genomes]
rs4687687	0.92[CEU][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap]
rs56019197	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56383738	0.80[ASN][1000 genomes]
rs60332615	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6445538	0.83[CHB][hapmap];0.82[CHD][hapmap]
rs6445539	0.83[CHB][hapmap];0.82[CHD][hapmap]
rs6445541	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6764322	0.83[EUR][1000 genomes]
rs6769789	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6773650	0.83[EUR][1000 genomes]
rs6795646	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap]
rs6803519	0.83[CHB][hapmap];0.82[CHD][hapmap]
rs7612624	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7617468	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7620690	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7626551	0.92[CEU][hapmap]
rs7630552	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7652667	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9682464	0.83[CHB][hapmap]
rs9810807	0.95[CEU][hapmap];0.91[CHB][hapmap]
rs9836499	0.96[CEU][hapmap];0.91[CHB][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9850563	0.96[CEU][hapmap];0.91[CHB][hapmap];0.81[AMR][1000 genomes]
rs9860296	0.96[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap]
rs9880978	0.96[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap]
rs9985365	0.87[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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:15)

SNP	Gene	Cis/trans	Tissue	Source
rs11922961	GLYCTK	cis	parietal	SCAN
rs11922961	ITIH4-AS1	cis	Artery Tibial	GTEx
rs11922961	NT5DC2	cis	lymphoblastoid	seeQTL
rs11922961	GNL3	cis	cerebellum	SCAN
rs11922961	GNL3	cis	parietal	SCAN
rs11922961	RFT1	cis	cerebellum	SCAN
rs11922961	ITIH4-AS1	cis	Muscle Skeletal	GTEx
rs11922961	WDR6	cis	cerebellum	SCAN
rs11922961	ITIH4	cis	lymphoblastoid	seeQTL
rs11922961	SEMA3G	cis	parietal	SCAN
rs11922961	NT5DC2	Cis_1M	lymphoblastoid	RTeQTL
rs11922961	TEX264	cis	parietal	SCAN
rs11922961	ITIH4-AS1	cis	lung	GTEx
rs11922961	ITIH4	cis	cerebellum	SCAN
rs11922961	ITIH4-AS1	cis	Artery Aorta	GTEx

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52852200-52869200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr3:52852800-52869200	Weak transcription	Primary B cells from cord blood	blood
3	chr3:52854200-52874200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:52854800-52869200	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr3:52854800-52888400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:52856000-52875000	Weak transcription	Fetal Intestine Large	intestine
7	chr3:52858800-52868800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr3:52858800-52868800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr3:52858800-52869200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr3:52859400-52869000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr3:52860200-52869000	Weak transcription	Fetal Intestine Small	intestine
12	chr3:52861200-52868800	Weak transcription	Lung	lung
13	chr3:52862000-52869200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr3:52862000-52882600	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr3:52863200-52872600	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr3:52864400-52875800	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr3:52865000-52869400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr3:52865200-52869000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr3:52865600-52874200	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr3:52865600-52875200	Weak transcription	Dnd41	blood
21	chr3:52865800-52869000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr3:52865800-52878600	Weak transcription	Small Intestine	intestine
23	chr3:52866000-52869800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr3:52866000-52884800	Weak transcription	HMEC	breast
25	chr3:52866200-52869000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr3:52866200-52869200	Weak transcription	Placenta	Placenta
27	chr3:52866200-52869600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr3:52866200-52870200	Weak transcription	Gastric	stomach
29	chr3:52866200-52872600	Weak transcription	Duodenum Mucosa	Duodenum
30	chr3:52866200-52872600	Weak transcription	Esophagus	oesophagus
31	chr3:52866200-52885200	Weak transcription	NHEK	skin
32	chr3:52866400-52868800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr3:52866400-52868800	Weak transcription	Colon Smooth Muscle	Colon
34	chr3:52866400-52869800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr3:52866400-52871800	Strong transcription	Primary T cells from cord blood	blood
36	chr3:52866400-52872400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr3:52866600-52868800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr3:52866600-52868800	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr3:52866600-52868800	Weak transcription	Adipose Nuclei	Adipose
40	chr3:52866600-52868800	Weak transcription	NHDF-Ad	bronchial
41	chr3:52866600-52868800	Weak transcription	NHLF	lung
42	chr3:52866600-52869800	Enhancers	Liver	Liver
43	chr3:52866600-52869800	Weak transcription	Brain Hippocampus Middle	brain
44	chr3:52866600-52873600	Weak transcription	Hela-S3	cervix
45	chr3:52866600-52879200	Weak transcription	Osteobl	bone
46	chr3:52866800-52871000	Strong transcription	Spleen	Spleen
47	chr3:52866800-52872000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr3:52866800-52876400	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr3:52866800-52878200	Strong transcription	Fetal Brain Female	brain
50	chr3:52866800-52879600	Genic enhancers	Fetal Thymus	thymus

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