Variant report

Variant	rs10940434
Chromosome Location	chr5:54174906-54174907
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10040872	0.91[ASN][1000 genomes]
rs10042734	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1005622	0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10056452	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10058862	0.80[EUR][1000 genomes]
rs10805469	0.84[EUR][1000 genomes]
rs10805470	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10940430	0.96[ASN][1000 genomes]
rs10940431	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10940432	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11738151	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11742711	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11953607	0.96[ASN][1000 genomes]
rs12515327	0.83[EUR][1000 genomes]
rs12657845	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13181749	0.97[ASN][1000 genomes]
rs1560165	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1560166	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1560167	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs17588816	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1965716	0.86[EUR][1000 genomes]
rs2017082	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2019005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2195392	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2195393	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28564901	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2897758	0.88[EUR][1000 genomes]
rs3916738	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3935813	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4242047	0.84[EUR][1000 genomes]
rs4242050	0.91[ASN][1000 genomes]
rs4320216	0.95[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs4446420	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4502767	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4865879	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4865880	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4865881	0.96[ASN][1000 genomes]
rs4865882	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6863705	0.84[CEU][hapmap];0.86[MEX][hapmap]
rs734097	0.85[EUR][1000 genomes]
rs737526	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7709516	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs976645	0.88[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	nsv830300	chr5:54056300-54257344	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv3358092	chr5:54077828-54189150	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv598179	chr5:54156269-54192823	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10940434	ARL15	cis	cerebellum	SCAN
rs10940434	ITGA2	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:54168600-54175600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:54170000-54178800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr5:54170800-54175800	Weak transcription	NHEK	skin
4	chr5:54171400-54176000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr5:54173200-54175200	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr5:54173200-54175600	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr5:54173200-54176600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr5:54173200-54178800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr5:54173400-54175400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr5:54173400-54175400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr5:54173400-54175400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr5:54173400-54175600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr5:54173400-54175600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr5:54173600-54175400	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr5:54174400-54179000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr5:54174600-54177000	Weak transcription	Osteobl	bone
17	chr5:54174800-54178600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links