Variant report

Variant	rs6495116
Chromosome Location	chr15:74885948-74885949
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:74885278..74889186-chr15:74890286..74893326,4	K562	blood:
2	chr15:74885692..74889192-chr15:74889315..74893477,4	MCF-7	breast:
3	chr15:74883645..74887048-chr15:74903468..74905388,3	MCF-7	breast:
4	chr15:74884721..74886383-chr15:74907313..74909259,2	MCF-7	breast:
5	chr15:74883904..74885997-chr15:74903287..74906186,2	MCF-7	breast:
6	chr15:74884059..74886045-chr15:74907649..74909590,2	K562	blood:
7	chr15:74884292..74886470-chr15:74890567..74893261,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260919	Chromatin interaction
ENSG00000179335	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1030889	0.83[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap]
rs10459601	0.92[GIH][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap]
rs10459648	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap]
rs10851871	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs10851873	0.82[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap]
rs11072489	0.82[MEX][hapmap]
rs11072492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap]
rs11072493	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs11072494	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap]
rs11072495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap]
rs11072496	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap]
rs11072497	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap]
rs11072498	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap]
rs11072499	0.86[GIH][hapmap];0.84[TSI][hapmap]
rs11629749	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap]
rs11629946	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.91[MEX][hapmap]
rs11854461	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap]
rs12439113	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12441932	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs12442097	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16969247	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs16969393	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs1866113	0.81[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap]
rs2068982	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap]
rs2198843	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs2289187	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs2289188	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs2415242	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap]
rs2899826	0.86[CHD][hapmap];0.92[GIH][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap]
rs3985310	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap]
rs4073149	0.87[CHD][hapmap];0.92[GIH][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap]
rs4886601	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap]
rs4887150	0.88[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap]
rs4887151	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4887152	0.89[CEU][hapmap];0.90[YRI][hapmap]
rs4887154	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4887159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap]
rs4887163	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap]
rs4887166	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs58473469	0.85[AFR][1000 genomes]
rs6495104	0.89[GIH][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap]
rs6495105	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6495106	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6495112	0.92[GIH][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap]
rs6495117	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs6495118	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs6495119	0.86[GIH][hapmap];0.84[TSI][hapmap]
rs6495121	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap]
rs7161903	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap]
rs7161990	0.87[CHD][hapmap];0.92[GIH][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap]
rs7163775	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs7166701	0.90[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs7171838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap]
rs7178568	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.91[MEX][hapmap]
rs7497036	0.92[GIH][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap]
rs7497342	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap]
rs750608	0.84[CHD][hapmap];0.84[GIH][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap]
rs8023479	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8023865	0.81[AFR][1000 genomes]
rs8026923	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8027066	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs8028430	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap]
rs8029116	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap]
rs8029215	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap]
rs8036030	0.86[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap]
rs8037211	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs8040120	0.92[GIH][hapmap];0.82[MEX][hapmap]
rs9635320	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap]
rs9672559	0.88[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1809847	chr15:74734500-74948063	Genic enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	esv1812223	chr15:74869438-74948063	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv904379	chr15:74869438-75027880	Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv904380	chr15:74869438-75142761	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
5	esv1814078	chr15:74884447-74948063	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
6	nsv457204	chr15:74885091-74948063	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	nsv569991	chr15:74885091-74948063	Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
8	nsv542434	chr15:74885329-74929552	Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS Strong transcription 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	39 gene(s)	inside rSNPs	diseases
9	nsv1047943	chr15:74885329-74940857	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6495116	SEMA7A	cis	cerebellum	SCAN
rs6495116	ARIH1	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74840600-74890400	Weak transcription	Stomach Mucosa	stomach
2	chr15:74845800-74890400	Weak transcription	A549	lung
3	chr15:74851800-74887800	Strong transcription	GM12878-XiMat	blood
4	chr15:74854800-74888600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr15:74857600-74888200	Strong transcription	Primary T helper cells PMA-I stimulated	--
6	chr15:74857800-74887600	Strong transcription	Primary T cells from cord blood	blood
7	chr15:74859000-74888600	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr15:74859600-74888000	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr15:74860400-74889000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr15:74860800-74888400	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr15:74861200-74889800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr15:74863600-74890800	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr15:74863800-74890400	Weak transcription	Psoas Muscle	Psoas
14	chr15:74864400-74887000	Strong transcription	Primary B cells from peripheral blood	blood
15	chr15:74864400-74888400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr15:74866800-74890800	Weak transcription	Ovary	ovary
17	chr15:74868400-74886800	Strong transcription	Fetal Intestine Small	intestine
18	chr15:74876600-74888800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr15:74877200-74888000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr15:74877400-74890400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr15:74877600-74887000	Strong transcription	Fetal Intestine Large	intestine
22	chr15:74877800-74888800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr15:74878000-74890200	Weak transcription	K562	blood
24	chr15:74878200-74887800	Strong transcription	Fetal Thymus	thymus
25	chr15:74878200-74888400	Strong transcription	Liver	Liver
26	chr15:74879800-74888000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr15:74881000-74886200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr15:74881000-74890400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr15:74881200-74888800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
30	chr15:74881200-74889600	Weak transcription	Fetal Heart	heart
31	chr15:74881200-74890400	Weak transcription	Fetal Kidney	kidney
32	chr15:74881200-74892200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr15:74881400-74888400	Strong transcription	Gastric	stomach
34	chr15:74881400-74889800	Strong transcription	Fetal Stomach	stomach
35	chr15:74881400-74890400	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr15:74881400-74890400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr15:74881400-74890400	Weak transcription	Fetal Brain Male	brain
38	chr15:74881400-74892200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr15:74881600-74888200	Strong transcription	H9 Cell Line	embryonic stem cell
40	chr15:74881600-74888400	Strong transcription	Rectal Mucosa Donor 29	rectum
41	chr15:74881600-74890400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr15:74881800-74886000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr15:74881800-74888000	Strong transcription	Duodenum Mucosa	Duodenum
44	chr15:74881800-74888000	Strong transcription	Fetal Muscle Trunk	muscle
45	chr15:74881800-74888400	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr15:74881800-74888400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
47	chr15:74881800-74888400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr15:74881800-74888400	Strong transcription	Brain Cingulate Gyrus	brain
49	chr15:74881800-74888800	Strong transcription	H1 Cell Line	embryonic stem cell
50	chr15:74881800-74888800	Strong transcription	Spleen	Spleen

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links