Variant report

Variant	rs2869442
Chromosome Location	chr4:87421278-87421279
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	chr4:87416425..87419552-chr4:87420696..87423306,3	K562	blood:

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10516775	0.87[EUR][1000 genomes]
rs10516776	0.87[EUR][1000 genomes]
rs1344260	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17011953	0.87[EUR][1000 genomes]
rs17011954	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes]
rs17011956	1.00[CEU][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs17011959	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes]
rs17011962	0.87[EUR][1000 genomes]
rs17011965	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes]
rs17011966	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs17011968	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs17011978	1.00[CEU][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs17011981	0.87[EUR][1000 genomes]
rs17011984	1.00[CEU][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs17011985	0.87[EUR][1000 genomes]
rs17011988	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs17011994	0.87[EUR][1000 genomes]
rs17012007	0.87[EUR][1000 genomes]
rs17012009	0.87[EUR][1000 genomes]
rs17012010	0.87[EUR][1000 genomes]
rs17012012	0.87[EUR][1000 genomes]
rs17012018	0.87[EUR][1000 genomes]
rs17419783	0.87[EUR][1000 genomes]
rs2170427	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];0.87[YRI][hapmap];0.87[EUR][1000 genomes]
rs2200052	0.87[EUR][1000 genomes]
rs2219993	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes]
rs28653505	0.90[EUR][1000 genomes]
rs2869443	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2904103	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34155193	0.87[EUR][1000 genomes]
rs35434858	0.87[EUR][1000 genomes]
rs4561893	1.00[CEU][hapmap];0.87[YRI][hapmap];0.87[EUR][1000 genomes]
rs4604024	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes]
rs4627823	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61121590	0.87[EUR][1000 genomes]
rs61344492	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72870675	0.87[EUR][1000 genomes]
rs72872208	0.87[EUR][1000 genomes]
rs72872209	0.87[EUR][1000 genomes]
rs7690137	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs980637	1.00[CEU][hapmap];0.87[YRI][hapmap];0.87[EUR][1000 genomes]
rs980638	1.00[CEU][hapmap];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594786	chr4:87076360-87609320	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
2	nsv999470	chr4:87165663-87514552	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	nsv537164	chr4:87165663-87514552	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
4	nsv594787	chr4:87221827-87888667	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv1012836	chr4:87279206-87643558	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
6	esv2757071	chr4:87417291-87689533	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
7	esv2759264	chr4:87417291-87689533	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2869442	GPM6A	trans	lymphoblastoid	seeQTL

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87407600-87422600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr4:87415000-87427000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr4:87417000-87421600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr4:87418200-87422000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr4:87418800-87429000	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr4:87419200-87421400	Enhancers	Pancreatic Islets	Pancreatic Islet
7	chr4:87419200-87421600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr4:87419600-87421400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr4:87419600-87421600	Weak transcription	NHLF	lung
10	chr4:87419600-87427400	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr4:87419600-87430600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr4:87420200-87421400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr4:87420200-87429200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr4:87420400-87422800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr4:87420400-87427600	Weak transcription	Fetal Kidney	kidney
16	chr4:87420600-87421600	Weak transcription	NHDF-Ad	bronchial
17	chr4:87420600-87421600	Weak transcription	NHEK	skin
18	chr4:87420600-87422800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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