Variant report

Variant	rs12629505
Chromosome Location	chr3:99904783-99904784
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10222474	0.90[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs12487143	0.86[CHB][hapmap]
rs12488245	0.80[JPT][hapmap]
rs2130369	0.86[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs2316263	1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.98[ASN][1000 genomes]
rs6767441	0.86[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs6776886	0.80[AFR][1000 genomes]
rs6798114	0.86[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs720688	0.83[ASN][1000 genomes]
rs7629487	0.86[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs9289981	0.86[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs9811920	0.86[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap]
rs9814549	0.86[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs9837131	0.86[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap]
rs9849632	0.82[ASN][1000 genomes]
rs9865713	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv1010897	chr3:99660754-99904783	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv591148	chr3:99774720-99905803	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12629505	C3orf26	cis	multi-tissue	Pritchard
rs12629505	SENP7	cis	parietal	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99899000-99907800	Weak transcription	Psoas Muscle	Psoas
2	chr3:99899000-99911000	Weak transcription	Aorta	Aorta
3	chr3:99902400-99905800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr3:99902600-99904800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr3:99902800-99905000	Enhancers	Fetal Stomach	stomach
6	chr3:99903000-99905600	Enhancers	NHDF-Ad	bronchial
7	chr3:99903200-99904800	Enhancers	Adipose Nuclei	Adipose
8	chr3:99903600-99904800	Enhancers	Fetal Lung	lung
9	chr3:99903800-99904800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr3:99903800-99905000	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr3:99903800-99905600	Enhancers	NHLF	lung
12	chr3:99903800-99906000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr3:99904000-99904800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr3:99904000-99904800	Enhancers	HSMMtube	muscle
15	chr3:99904000-99905400	Enhancers	Placenta	Placenta
16	chr3:99904200-99904800	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr3:99904200-99904800	Enhancers	Sigmoid Colon	Sigmoid Colon
18	chr3:99904200-99905000	Enhancers	Left Ventricle	heart
19	chr3:99904200-99905000	Enhancers	Right Atrium	heart
20	chr3:99904200-99905000	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr3:99904200-99905000	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr3:99904200-99905000	Enhancers	Spleen	Spleen
23	chr3:99904200-99905600	Enhancers	Fetal Muscle Leg	muscle
24	chr3:99904200-99905600	Enhancers	Ovary	ovary
25	chr3:99904400-99904800	Enhancers	Fetal Kidney	kidney
26	chr3:99904600-99904800	Enhancers	Placenta Amnion	Placenta Amnion
27	chr3:99904600-99905000	Enhancers	Right Ventricle	heart
28	chr3:99904600-99905400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr3:99904600-99905800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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