Variant report

Variant	rs10863988
Chromosome Location	chr1:212894474-212894475
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:212883928..212885443-chr1:212893940..212896251,2	K562	blood:
2	chr1:212836810..212838698-chr1:212893366..212895753,2	K562	blood:

Extended variants
information (count: 73 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1046083	0.83[ASN][1000 genomes]
rs10863989	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10863997	0.84[GIH][hapmap];0.89[MEX][hapmap]
rs11120001	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11120006	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11120007	0.83[ASN][1000 genomes]
rs11120010	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11120014	0.87[ASW][hapmap];0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11120018	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11120029	0.81[GIH][hapmap]
rs11800642	0.83[ASN][1000 genomes]
rs11806535	0.81[ASN][1000 genomes]
rs11808846	0.87[ASW][hapmap];0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11810895	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11811017	0.81[ASN][1000 genomes]
rs12119531	0.88[ASN][1000 genomes]
rs12125867	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12128410	0.81[GIH][hapmap]
rs12128903	0.83[ASN][1000 genomes]
rs12129465	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12133174	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12139618	0.88[ASN][1000 genomes]
rs12145131	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12404618	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12404885	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12409787	0.95[EUR][1000 genomes]
rs12729663	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs13376383	0.83[CHB][hapmap]
rs1507357	0.84[GIH][hapmap];0.81[ASN][1000 genomes]
rs1507358	0.87[ASW][hapmap];0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1532951	0.81[GIH][hapmap]
rs17019726	0.81[GIH][hapmap];0.80[TSI][hapmap]
rs1857971	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2135823	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2174780	0.83[ASN][1000 genomes]
rs2174781	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2271148	0.81[GIH][hapmap];0.83[ASN][1000 genomes]
rs2358899	0.81[ASN][1000 genomes]
rs28872849	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3738798	0.87[ASW][hapmap];0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3738803	0.83[CHB][hapmap];0.84[GIH][hapmap];0.88[MEX][hapmap]
rs58203936	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59231663	0.83[ASN][1000 genomes]
rs60308869	0.83[ASN][1000 genomes]
rs61736926	0.87[ASN][1000 genomes]
rs6540760	0.83[ASN][1000 genomes]
rs6540762	0.87[ASW][hapmap];0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6657089	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6662981	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6664049	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6665365	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6681171	0.83[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6687672	0.84[GIH][hapmap];0.89[MEX][hapmap]
rs6694190	0.83[CEU][hapmap]
rs6694448	0.83[ASN][1000 genomes]
rs6702101	0.87[ASW][hapmap];0.90[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.84[JPT][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73081830	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73081853	0.81[ASN][1000 genomes]
rs73083705	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7516312	0.84[GIH][hapmap]
rs7525518	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7527216	0.83[ASN][1000 genomes]
rs7536456	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7536629	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7537598	0.82[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7546462	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7546564	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7546754	0.83[ASN][1000 genomes]
rs7550288	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7552899	0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013110	chr1:212555764-212948092	Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
2	nsv535287	chr1:212555764-212948092	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
3	nsv549148	chr1:212876902-212962207	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs10863988	SLC30A1	cis	parietal	SCAN
rs10863988	LOC642946	cis	multi-tissue	Pritchard
rs10863988	SNFT	cis	multi-tissue	Pritchard
rs10863988	NSL1	cis	parietal	SCAN
rs10863988	BATF3	cis	cerebellum	SCAN
rs10863988	TATDN3	cis	multi-tissue	Pritchard
rs10863988	HSD11B1	cis	cerebellum	SCAN
rs10863988	TATDN3	cis	Adipose Subcutaneous	GTEx
rs10863988	IL20	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212892000-212894600	Weak transcription	A549	lung
2	chr1:212892000-212894600	Weak transcription	NHDF-Ad	bronchial
3	chr1:212892200-212894600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:212892800-212894600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr1:212894200-212894600	Enhancers	HepG2	liver
6	chr1:212894400-212894600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
7	chr1:212894400-212894600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr1:212894400-212894600	Enhancers	GM12878-XiMat	blood
9	chr1:212894400-212894600	Enhancers	NHEK	skin
10	chr1:212894400-212894600	Enhancers	Osteobl	bone
11	chr1:212894400-212894800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr1:212894400-212895000	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr1:212894400-212897200	Enhancers	Primary hematopoietic stem cells short term culture	blood

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