Variant report

Variant	rs3901950
Chromosome Location	chr1:186467274-186467275
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:186462234..186463900-chr1:186466419..186468938,2	MCF-7	breast:

Extended variants
information (count: 86 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10798041	0.82[ASW][hapmap];0.90[YRI][hapmap]
rs10798048	0.80[YRI][hapmap]
rs10798051	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10911864	0.90[YRI][hapmap]
rs10911866	0.90[YRI][hapmap]
rs10911869	0.91[AFR][1000 genomes]
rs10911877	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.96[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10911878	0.82[CEU][hapmap];0.81[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10911886	0.82[ASW][hapmap];0.80[YRI][hapmap]
rs10911888	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10911890	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10911892	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10911895	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11580808	0.86[EUR][1000 genomes]
rs11582183	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11803944	0.82[JPT][hapmap]
rs11805124	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11812050	0.82[JPT][hapmap]
rs12071770	0.84[AFR][1000 genomes]
rs12087470	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12089415	0.92[AFR][1000 genomes]
rs12093901	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12402521	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12404145	0.89[YRI][hapmap]
rs12406189	0.91[AFR][1000 genomes]
rs12406209	0.91[AFR][1000 genomes]
rs12407957	0.82[ASW][hapmap];0.90[YRI][hapmap]
rs12409263	0.90[AFR][1000 genomes]
rs12410237	0.91[AFR][1000 genomes]
rs12728706	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12750371	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16825403	0.82[JPT][hapmap]
rs16825434	0.80[ASN][1000 genomes]
rs16825469	0.84[AFR][1000 genomes]
rs1799957	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1929092	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1929095	0.82[ASW][hapmap]
rs2008704	0.81[ASN][1000 genomes]
rs2024761	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2180167	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2207727	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2383385	0.92[AFR][1000 genomes]
rs2383508	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34396375	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34869216	0.90[AFR][1000 genomes]
rs35643079	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35868587	0.80[ASN][1000 genomes]
rs35999012	0.90[AFR][1000 genomes]
rs36105782	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3844242	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3851884	0.91[AFR][1000 genomes]
rs3901243	0.82[ASN][1000 genomes]
rs3934200	0.91[AFR][1000 genomes]
rs4140433	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4567244	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57390268	0.87[AFR][1000 genomes]
rs59547074	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6425035	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6659683	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6666413	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6666813	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6672836	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6675505	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6677346	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6679923	0.90[AFR][1000 genomes]
rs6680252	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6689065	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6689727	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6692629	0.91[AFR][1000 genomes]
rs6694957	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72719487	0.92[AFR][1000 genomes]
rs72719501	0.84[AFR][1000 genomes]
rs7512750	0.82[ASW][hapmap];0.80[YRI][hapmap]
rs7518525	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7523747	0.84[AFR][1000 genomes]
rs7525586	0.89[AFR][1000 genomes]
rs7526069	0.84[AFR][1000 genomes]
rs7534971	0.82[AFR][1000 genomes]
rs7536199	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7555973	0.91[AFR][1000 genomes]
rs7556360	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]

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	nsv1004481	chr1:186095854-186750968	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv535223	chr1:186095854-186750968	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv1012164	chr1:186323867-186565995	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	esv2762201	chr1:186323879-186566007	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv832059	chr1:186464932-186639125	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3901950	C1orf14	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:186452200-186467800	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr1:186452400-186468400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr1:186459400-186471800	Weak transcription	Brain Angular Gyrus	brain
4	chr1:186462600-186467400	Weak transcription	Stomach Mucosa	stomach
5	chr1:186462600-186469600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr1:186462800-186467400	Weak transcription	Osteobl	bone
7	chr1:186462800-186467600	Weak transcription	Hela-S3	cervix
8	chr1:186462800-186468000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr1:186464200-186469600	Weak transcription	Aorta	Aorta
10	chr1:186464800-186467600	Weak transcription	HMEC	breast
11	chr1:186465000-186467800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr1:186465200-186467400	Weak transcription	NHEK	skin
13	chr1:186465400-186467600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr1:186465400-186467600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:186465400-186468000	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr1:186465400-186468600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr1:186466000-186467600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr1:186466400-186471000	Weak transcription	Brain Anterior Caudate	brain
19	chr1:186466600-186470600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr1:186467000-186471000	Weak transcription	GM12878-XiMat	blood
21	chr1:186467000-186471400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr1:186467200-186467400	Enhancers	iPS-20b Cell Line	embryonic stem cell
23	chr1:186467200-186468000	Flanking Active TSS	A549	lung
24	chr1:186467200-186468800	Enhancers	NH-A	brain
25	chr1:186467200-186470200	Enhancers	HUVEC	blood vessel
26	chr1:186467200-186471200	Weak transcription	Brain Cingulate Gyrus	brain
27	chr1:186467200-186474400	Enhancers	NHDF-Ad	bronchial

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