Variant report

Variant	rs6689727
Chromosome Location	chr1:186461603-186461604
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	chr1:186459487..186462134-chr1:186462680..186465381,2	K562	blood:

Extended variants
information (count: 92 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10798041	0.82[ASW][hapmap];0.90[YRI][hapmap]
rs10798048	0.80[YRI][hapmap]
rs10798051	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10911864	0.90[YRI][hapmap]
rs10911866	0.90[YRI][hapmap]
rs10911869	0.92[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];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10911878	0.82[CEU][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10911886	0.82[ASW][hapmap];0.80[YRI][hapmap]
rs10911888	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10911890	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10911892	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10911895	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11580808	0.84[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];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11800651	0.81[ASN][1000 genomes]
rs11803944	0.82[JPT][hapmap]
rs11805124	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11806017	0.81[ASN][1000 genomes]
rs11812050	0.82[JPT][hapmap]
rs12071770	0.83[AFR][1000 genomes]
rs12087470	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12089415	0.91[AFR][1000 genomes]
rs12093901	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12402521	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12404145	0.89[YRI][hapmap]
rs12406189	0.92[AFR][1000 genomes]
rs12406209	0.92[AFR][1000 genomes]
rs12407957	0.82[ASW][hapmap];0.90[YRI][hapmap]
rs12409263	0.91[AFR][1000 genomes]
rs12410237	0.92[AFR][1000 genomes]
rs12728706	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12750371	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16825403	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs16825434	0.82[ASN][1000 genomes]
rs16825469	0.83[AFR][1000 genomes]
rs1799957	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1929092	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1929095	0.82[ASW][hapmap]
rs2024761	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2180167	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2207727	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2383385	0.91[AFR][1000 genomes]
rs2383508	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs33963275	0.81[ASN][1000 genomes]
rs34228564	0.81[ASN][1000 genomes]
rs34396375	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34781399	0.81[ASN][1000 genomes]
rs34869216	0.91[AFR][1000 genomes]
rs35643079	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35868587	0.82[ASN][1000 genomes]
rs35945739	0.81[ASN][1000 genomes]
rs35999012	0.90[AFR][1000 genomes]
rs36105782	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3844242	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3851884	0.91[AFR][1000 genomes]
rs3901243	0.80[ASN][1000 genomes]
rs3901950	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3933210	0.81[ASN][1000 genomes]
rs3934200	0.92[AFR][1000 genomes]
rs4140433	0.89[AMR][1000 genomes];0.87[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];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57390268	0.87[AFR][1000 genomes]
rs59547074	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6425035	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6659683	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6666413	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6666813	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[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];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6675505	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[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];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6679923	0.91[AFR][1000 genomes]
rs6680252	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6689065	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6692629	0.92[AFR][1000 genomes]
rs6694957	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs71634164	0.81[ASN][1000 genomes]
rs72719487	0.91[AFR][1000 genomes]
rs72719501	0.83[AFR][1000 genomes]
rs7512750	0.82[ASW][hapmap];0.80[YRI][hapmap]
rs7518525	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7523747	0.83[AFR][1000 genomes]
rs7525586	0.88[AFR][1000 genomes]
rs7526069	0.83[AFR][1000 genomes]
rs7534971	0.81[AFR][1000 genomes]
rs7536199	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7555973	0.92[AFR][1000 genomes]
rs7556360	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6689727	C1orf14	cis	parietal	SCAN

Chromatin state (count:13 , 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	chr1:186456000-186461800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr1:186457400-186462000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:186458000-186462200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr1:186459400-186471800	Weak transcription	Brain Angular Gyrus	brain
7	chr1:186459600-186462200	Weak transcription	NHEK	skin
8	chr1:186461400-186461800	Enhancers	Osteobl	bone
9	chr1:186461600-186462000	Enhancers	Hela-S3	cervix
10	chr1:186461600-186462200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:186461600-186462200	Active TSS	A549	lung
12	chr1:186461600-186462200	Flanking Active TSS	HUVEC	blood vessel
13	chr1:186461600-186462600	Enhancers	Stomach Mucosa	stomach

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