Variant report

Variant	rs7765656
Chromosome Location	chr6:55270581-55270582
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10807491	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10948915	0.96[ASN][1000 genomes]
rs12201786	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12205513	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12529201	0.87[ASN][1000 genomes]
rs1472637	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1472638	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1502199	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1502200	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1502201	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1546296	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1546297	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17750667	0.94[ASN][1000 genomes]
rs4145282	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4715541	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4715542	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4715543	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4715549	0.82[CHB][hapmap]
rs6900273	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6912623	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6913781	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6918921	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6920497	0.86[CEU][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6936510	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9349778	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9367634	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9370418	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9382490	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9396088	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885903	chr6:55142337-55344782	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv885904	chr6:55156812-55344782	Enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1034037	chr6:55222409-56069600	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv470819	chr6:55236937-55368815	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1031179	chr6:55237283-55372905	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv1029436	chr6:55237283-55386038	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv1028560	chr6:55237723-55378113	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv1024550	chr6:55237723-55387481	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv462948	chr6:55238091-55368815	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv603163	chr6:55238091-55368815	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv5311	chr6:55259390-55304045	Enhancers Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7765656	ICK	cis	cerebellum	SCAN
rs7765656	GSTA1	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:55269800-55270800	Enhancers	Fetal Stomach	stomach
2	chr6:55270200-55271000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr6:55270200-55271200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr6:55270400-55271400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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