Variant report

Variant	rs10866441
Chromosome Location	chr4:57820120-57820121
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:57818770..57822763-chr4:57823881..57826643,6	K562	blood:
2	chr4:57818504..57821226-chr4:57843903..57845654,2	K562	blood:
3	chr4:57819778..57821428-chr4:57822188..57824307,2	MCF-7	breast:
4	chr4:57797516..57799149-chr4:57818426..57821000,2	K562	blood:

Variant related genes	Relation type
ENSG00000047315	Chromatin interaction
ENSG00000084092	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10008356	0.80[ASN][1000 genomes]
rs10030913	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10866440	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1105434	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1107675	0.94[CHB][hapmap];0.80[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11133472	0.87[GIH][hapmap];0.90[TSI][hapmap]
rs11133474	0.83[GIH][hapmap];0.90[TSI][hapmap]
rs11729152	0.86[ASN][1000 genomes]
rs11730321	0.94[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap]
rs11730525	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11734953	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11736808	0.82[ASN][1000 genomes]
rs11736869	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11736965	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11737689	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11932673	0.94[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11933908	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12500454	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12501224	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12501990	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12502076	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1277271	0.80[ASN][1000 genomes]
rs1277287	1.00[JPT][hapmap]
rs13108245	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13113802	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13116564	0.84[ASN][1000 genomes]
rs13119525	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13123018	0.86[EUR][1000 genomes]
rs13131605	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13136432	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13146539	0.84[ASN][1000 genomes]
rs13146960	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13149162	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13150593	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13152476	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13353552	0.83[ASN][1000 genomes]
rs1625691	1.00[JPT][hapmap]
rs17081937	1.00[JPT][hapmap]
rs17087307	0.84[ASN][1000 genomes]
rs17087317	0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs17087411	0.87[JPT][hapmap]
rs17087414	0.87[JPT][hapmap]
rs1718839	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1877669	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1963666	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1976780	0.84[ASN][1000 genomes]
rs2002153	0.81[ASN][1000 genomes]
rs2014870	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2090962	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2170073	0.82[CEU][hapmap]
rs2228991	0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2412772	0.96[CEU][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes]
rs3000	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34124552	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34448457	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34659774	0.84[ASN][1000 genomes]
rs35267092	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3733306	0.89[CHB][hapmap];0.93[JPT][hapmap]
rs3796528	0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs3806745	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs4276341	0.84[ASN][1000 genomes]
rs4339274	0.82[CEU][hapmap]
rs4864606	0.87[ASN][1000 genomes]
rs4864607	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4864608	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4865159	0.81[ASN][1000 genomes]
rs4865160	0.81[ASN][1000 genomes]
rs4865172	0.88[CEU][hapmap]
rs55822707	0.85[ASN][1000 genomes]
rs62308135	0.87[ASN][1000 genomes]
rs62308136	0.87[ASN][1000 genomes]
rs62308137	0.86[ASN][1000 genomes]
rs62308155	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6554397	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6554398	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6554399	0.86[ASN][1000 genomes]
rs6816457	0.80[ASN][1000 genomes]
rs6838948	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.94[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6847086	0.82[JPT][hapmap]
rs6852110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6854420	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6855212	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs729844	0.84[ASN][1000 genomes]
rs73242609	0.87[ASN][1000 genomes]
rs73242616	0.84[ASN][1000 genomes]
rs7661194	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs7666804	0.84[ASN][1000 genomes]
rs7667302	0.84[ASN][1000 genomes]
rs7680140	0.82[CEU][hapmap];0.92[MEX][hapmap]
rs7680734	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7685576	0.84[ASN][1000 genomes]
rs7695970	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7697176	0.82[CEU][hapmap];0.80[AMR][1000 genomes]
rs781665	0.81[ASN][1000 genomes]
rs781666	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs781668	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs781669	0.88[ASN][1000 genomes]
rs899632	0.84[ASN][1000 genomes]
rs9684742	0.84[ASN][1000 genomes]
rs9685436	0.82[CEU][hapmap]
rs9942208	0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv1012287	chr4:57652778-57853485	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv1012125	chr4:57668229-57865803	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	esv3425352	chr4:57783591-57820951	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10866441	RP11-738E22.3	cis	Esophagus Mucosa	GTEx
rs10866441	TXNDC9	cis	parietal	SCAN
rs10866441	IGFBP7	cis	multi-tissue	Pritchard
rs10866441	KIAA1211	cis	parietal	SCAN
rs10866441	RP11-738E22.3	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57793600-57842000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr4:57793600-57842000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr4:57798200-57828400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr4:57798200-57829600	Weak transcription	Pancreas	Pancrea
5	chr4:57798400-57828200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr4:57798600-57828200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr4:57803800-57828400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr4:57804200-57824200	Weak transcription	NH-A	brain
9	chr4:57804800-57826600	Weak transcription	Liver	Liver
10	chr4:57805000-57830800	Weak transcription	Colonic Mucosa	Colon
11	chr4:57805400-57826400	Weak transcription	Primary T cells from cord blood	blood
12	chr4:57805600-57826600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr4:57805800-57827400	Weak transcription	Placenta	Placenta
14	chr4:57806000-57827000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr4:57806000-57827200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr4:57806000-57827200	Weak transcription	Thymus	Thymus
17	chr4:57806200-57826600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr4:57806200-57827400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr4:57808200-57827200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr4:57808600-57827000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr4:57818800-57826800	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr4:57818800-57827200	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr4:57818800-57827400	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr4:57819000-57828400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr4:57819400-57827200	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr4:57819600-57826600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr4:57819800-57820400	Enhancers	Brain Substantia Nigra	brain
28	chr4:57819800-57821200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr4:57819800-57821600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr4:57820000-57820200	ZNF genes & repeats	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr4:57820000-57820200	Enhancers	Brain Anterior Caudate	brain
32	chr4:57820000-57820200	Flanking Active TSS	Brain Hippocampus Middle	brain
33	chr4:57820000-57820200	Enhancers	Esophagus	oesophagus
34	chr4:57820000-57820400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr4:57820000-57820600	Active TSS	Brain Cingulate Gyrus	brain
36	chr4:57820000-57820600	Active TSS	Brain Inferior Temporal Lobe	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links