Variant report

Variant	rs2952556
Chromosome Location	chr7:120927792-120927793
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10231005	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10233441	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10241888	1.00[CEU][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes]
rs10276111	1.00[CEU][hapmap];0.86[TSI][hapmap];0.88[EUR][1000 genomes]
rs10276127	0.82[EUR][1000 genomes]
rs10277699	0.90[EUR][1000 genomes]
rs10282303	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12534075	0.83[CEU][hapmap]
rs1547959	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1547960	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2707520	0.82[ASN][1000 genomes]
rs2707521	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34155977	0.90[EUR][1000 genomes]
rs35883000	0.90[EUR][1000 genomes]
rs6947246	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6952851	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6961083	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6980043	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7778200	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7794940	0.90[EUR][1000 genomes]
rs7795061	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs7809135	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs798906	0.83[CEU][hapmap]
rs798907	0.83[CEU][hapmap]

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	nsv1025430	chr7:120638930-121179289	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv427802	chr7:120749159-120935856	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	nsv1034353	chr7:120818382-121040576	Enhancers Bivalent Enhancer Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS 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 target site	19 gene(s)	inside rSNPs	diseases
4	nsv1026322	chr7:120841937-121188037	Weak transcription Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv539102	chr7:120841937-121188037	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	esv2755350	chr7:120848049-121119049	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv1027619	chr7:120906437-120976630	Enhancers Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
8	esv2757237	chr7:120908459-120993326	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
9	esv2759558	chr7:120908459-120993326	Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
10	nsv1032054	chr7:120926379-121432971	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
11	nsv539103	chr7:120926379-121432971	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2952556	FLJ21986	cis	multi-tissue	Pritchard
rs2952556	LMOD2	cis	parietal	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:120872600-120936600	Weak transcription	Psoas Muscle	Psoas
2	chr7:120888800-120937800	Weak transcription	Colon Smooth Muscle	Colon
3	chr7:120909000-120933000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr7:120910200-120930000	Weak transcription	Fetal Lung	lung
5	chr7:120910200-120933200	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr7:120920600-120935400	Weak transcription	HSMMtube	muscle
7	chr7:120924000-120927800	ZNF genes & repeats	Primary B cells from peripheral blood	blood
8	chr7:120924200-120930000	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr7:120925200-120929600	Strong transcription	K562	blood
10	chr7:120925400-120932800	Weak transcription	Fetal Stomach	stomach
11	chr7:120925400-120932800	Weak transcription	Right Ventricle	heart
12	chr7:120925400-120935600	Weak transcription	Fetal Heart	heart
13	chr7:120925600-120929000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr7:120925600-120934400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr7:120926200-120930000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr7:120926200-120941000	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr7:120926600-120937600	Weak transcription	Ovary	ovary
18	chr7:120926800-120930000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr7:120927000-120927800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr7:120927000-120928800	Enhancers	HMEC	breast
21	chr7:120927200-120928000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr7:120927200-120929200	Enhancers	NHDF-Ad	bronchial
23	chr7:120927200-120929400	Enhancers	NHLF	lung
24	chr7:120927200-120929600	Enhancers	NH-A	brain
25	chr7:120927200-120929800	Enhancers	Muscle Satellite Cultured Cells	--
26	chr7:120927400-120927800	Enhancers	HSMM	muscle
27	chr7:120927400-120928000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr7:120927400-120929400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr7:120927400-120929600	Enhancers	Osteobl	bone
30	chr7:120927400-120929800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr7:120927400-120933400	Weak transcription	Aorta	Aorta
32	chr7:120927400-120933800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr7:120927600-120928400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr7:120927600-120928400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr7:120927600-120929000	Weak transcription	NHEK	skin
36	chr7:120927600-120930000	Weak transcription	Adipose Nuclei	Adipose
37	chr7:120927600-120933200	Weak transcription	Left Ventricle	heart
38	chr7:120927600-120933400	Weak transcription	Stomach Smooth Muscle	stomach
39	chr7:120927600-120935200	Weak transcription	Liver	Liver
40	chr7:120927600-120935600	Weak transcription	Skeletal Muscle Female	skeletal muscle

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