Variant report

Variant	rs2176473
Chromosome Location	chr1:169331802-169331803
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:169331328..169334287-chr1:169334911..169337205,2	MCF-7	breast:
2	chr1:169327940..169332501-chr1:169336019..169339615,5	K562	blood:
3	chr1:169075705..169078397-chr1:169329097..169333069,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000117475	Chromatin interaction
ENSG00000143153	Chromatin interaction
ENSG00000143156	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1018831	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10429893	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10465575	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10465576	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10489189	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10732287	0.87[CHD][hapmap];0.82[JPT][hapmap]
rs10753786	0.85[CEU][hapmap];0.93[YRI][hapmap]
rs10800408	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap]
rs10800424	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs10800425	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs10800435	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10800438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800439	0.85[CEU][hapmap]
rs10800440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919120	0.86[ASW][hapmap];0.88[CHD][hapmap]
rs10919124	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs10919132	0.85[CEU][hapmap];0.93[YRI][hapmap]
rs10919168	0.81[ASN][1000 genomes]
rs10919174	0.82[JPT][hapmap]
rs1124843	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1133814	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1200079	0.82[JPT][hapmap]
rs1200083	0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.96[YRI][hapmap]
rs1200085	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs12029566	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12076993	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1208134	0.81[ASN][1000 genomes]
rs1208135	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs1208370	0.87[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.94[MEX][hapmap];0.85[TSI][hapmap];0.96[YRI][hapmap]
rs1208377	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.85[TSI][hapmap];0.92[YRI][hapmap]
rs1400836	0.81[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.93[MKK][hapmap];0.84[TSI][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1517744	0.87[CHD][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs1517747	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs1591733	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.85[TSI][hapmap];0.96[YRI][hapmap]
rs16861990	0.82[JPT][hapmap]
rs1856303	0.89[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs1914505	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1983546	0.87[CHD][hapmap];0.82[JPT][hapmap]
rs2003653	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2037250	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.96[YRI][hapmap]
rs2138898	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2176474	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2300158	0.85[CEU][hapmap];0.93[YRI][hapmap]
rs3766057	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3766095	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs3820059	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3905328	0.81[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.93[MKK][hapmap];0.84[TSI][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4264046	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs4454599	0.84[AMR][1000 genomes]
rs4656183	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4656672	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6427185	0.81[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.93[MKK][hapmap];0.82[TSI][hapmap];0.89[YRI][hapmap]
rs6427187	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6656822	0.87[CHD][hapmap];0.82[JPT][hapmap]
rs6669901	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6700375	0.81[ASN][1000 genomes]
rs7415756	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7521582	0.87[ASW][hapmap];1.00[CHD][hapmap]
rs7533257	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.85[TSI][hapmap];0.96[YRI][hapmap]
rs7535765	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7544221	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7554689	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs760603	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs925892	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs932301	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs994986	1.00[CHB][hapmap];0.82[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	esv3522071	chr1:168978325-169339044	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	esv3522072	chr1:168978325-169339044	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv1010010	chr1:169189586-169347545	Active TSS Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv872531	chr1:169191860-169388193	Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv872532	chr1:169275630-169363203	Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv831871	chr1:169320673-169486680	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs2176473	NME7	cis	Nerve Tibial	GTEx
rs2176473	NME7	cis	Stomach	GTEx
rs2176473	NME7	cis	Thyroid	GTEx
rs2176473	C1orf114	cis	cerebellum	SCAN
rs2176473	KIFAP3	cis	cerebellum	SCAN
rs2176473	NME7	cis	Artery Aorta	GTEx
rs2176473	NME7	cis	Esophagus Muscularis	GTEx
rs2176473	SELP	cis	cerebellum	SCAN
rs2176473	NME7	cis	multi-tissue	Pritchard
rs2176473	SCYL3	cis	parietal	SCAN
rs2176473	NME7	Cis_1M	lymphoblastoid	RTeQTL
rs2176473	NME7	cis	parietal	SCAN
rs2176473	NME7	cis	Artery Tibial	GTEx

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169270200-169336400	Weak transcription	Stomach Smooth Muscle	stomach
2	chr1:169305600-169336400	Weak transcription	Left Ventricle	heart
3	chr1:169309200-169333600	Weak transcription	Primary hematopoietic stem cells	blood
4	chr1:169309400-169336400	Weak transcription	Ovary	ovary
5	chr1:169310800-169332800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr1:169311000-169336400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:169316000-169334200	Weak transcription	Fetal Intestine Small	intestine
8	chr1:169317000-169336400	Weak transcription	Pancreas	Pancrea
9	chr1:169317200-169333800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr1:169317800-169332800	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr1:169317800-169333800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr1:169317800-169335800	Weak transcription	Fetal Lung	lung
13	chr1:169318000-169332200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr1:169318200-169334000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr1:169324600-169335800	Weak transcription	Primary T cells from cord blood	blood
16	chr1:169325600-169335800	Weak transcription	K562	blood
17	chr1:169326200-169334200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr1:169327200-169335800	Weak transcription	Small Intestine	intestine
19	chr1:169327200-169336200	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr1:169328400-169332800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr1:169329800-169332200	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr1:169330000-169332600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr1:169330000-169336400	Weak transcription	Psoas Muscle	Psoas
24	chr1:169330200-169332800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr1:169330800-169335800	Weak transcription	Brain Hippocampus Middle	brain
26	chr1:169330800-169336400	Weak transcription	Right Ventricle	heart
27	chr1:169331000-169332000	Weak transcription	GM12878-XiMat	blood
28	chr1:169331000-169332600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr1:169331400-169335800	Weak transcription	Fetal Intestine Large	intestine
30	chr1:169331600-169333200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr1:169331600-169333400	Enhancers	Osteobl	bone
32	chr1:169331600-169335600	Enhancers	HMEC	breast
33	chr1:169331800-169332000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr1:169331800-169332000	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr1:169331800-169332000	ZNF genes & repeats	HSMM	muscle
36	chr1:169331800-169332000	Genic enhancers	NHEK	skin
37	chr1:169331800-169332000	Enhancers	NHLF	lung
38	chr1:169331800-169332800	Enhancers	Hela-S3	cervix
39	chr1:169331800-169332800	Enhancers	NH-A	brain
40	chr1:169331800-169333000	Enhancers	Placenta Amnion	Placenta Amnion
41	chr1:169331800-169333000	Enhancers	NHDF-Ad	bronchial
42	chr1:169331800-169333200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
43	chr1:169331800-169333400	Enhancers	Muscle Satellite Cultured Cells	--
44	chr1:169331800-169333400	Enhancers	HUVEC	blood vessel
45	chr1:169331800-169333600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr1:169331800-169335800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr1:169331800-169336200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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