Variant report

Variant	rs532859
Chromosome Location	chr11:107479652-107479653
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10890744	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10890745	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10890746	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11212292	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.90[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1261740	0.97[ASN][1000 genomes]
rs1939903	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2509204	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3132818	0.92[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4085361	0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.87[YRI][hapmap];0.93[ASN][1000 genomes]
rs4754234	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4754235	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4754236	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4754237	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs531097	1.00[ASW][hapmap];0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs537974	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs539814	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs602788	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs614759	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs651300	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6588970	0.92[CHB][hapmap];0.94[CHD][hapmap];0.89[MEX][hapmap];0.82[ASN][1000 genomes]
rs7943671	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7943986	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038368	chr11:107116577-107664181	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv541163	chr11:107116577-107664181	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv556376	chr11:107250851-107486598	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv533794	chr11:107349817-108093259	Bivalent Enhancer Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv1039425	chr11:107468681-107895836	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv427899	chr11:107471544-107805894	Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	nsv468866	chr11:107472733-107566585	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv556377	chr11:107472733-107566585	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	esv2422201	chr11:107479362-107555825	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs532859	LOC643923	cis	uninvolved skin	skin_eQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:107463200-107482600	Weak transcription	HSMMtube	muscle
2	chr11:107477200-107480400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr11:107478400-107481000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr11:107478600-107481000	Enhancers	HUVEC	blood vessel
5	chr11:107478800-107480400	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr11:107478800-107480400	Enhancers	iPS-20b Cell Line	embryonic stem cell
7	chr11:107479000-107480000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr11:107479000-107480600	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr11:107479000-107480600	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr11:107479000-107481000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr11:107479200-107479800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
12	chr11:107479200-107481000	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
13	chr11:107479400-107480200	Enhancers	Liver	Liver
14	chr11:107479400-107481200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr11:107479600-107479800	Enhancers	H1 Cell Line	embryonic stem cell
16	chr11:107479600-107479800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
17	chr11:107479600-107480600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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