Variant report

Variant	rs7609779
Chromosome Location	chr3:100529700-100529701
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11716316	0.85[JPT][hapmap]
rs12496951	0.84[CHD][hapmap];0.82[JPT][hapmap];0.85[YRI][hapmap]
rs12696195	0.81[CHB][hapmap]
rs1394077	1.00[CEU][hapmap];0.80[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.93[MEX][hapmap];0.95[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1503839	0.84[CHD][hapmap];0.82[JPT][hapmap]
rs1503845	0.84[CHD][hapmap];0.82[JPT][hapmap]
rs16842822	0.95[CHB][hapmap];0.91[CHD][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs16842845	0.84[CHD][hapmap];0.82[JPT][hapmap]
rs1847391	0.82[JPT][hapmap]
rs3736534	0.87[CHD][hapmap]
rs544500	0.87[CHD][hapmap]
rs754462	0.86[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7612334	0.85[JPT][hapmap]
rs7613610	0.84[CEU][hapmap];0.91[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7632038	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.86[MKK][hapmap];0.92[TSI][hapmap];0.85[YRI][hapmap];0.93[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7634500	0.81[YRI][hapmap]
rs7642942	0.86[CHB][hapmap];0.94[CHD][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs764684	0.84[CHD][hapmap];0.82[JPT][hapmap]
rs9824346	0.82[JPT][hapmap]
rs983474	1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9842968	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9850273	0.84[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs989793	0.85[JPT][hapmap]
rs989794	0.82[JPT][hapmap]
rs989795	0.84[CHD][hapmap];0.82[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1798221	chr3:100518650-100536284	Genic enhancers Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7609779	FAM55C	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100502400-100530400	Weak transcription	Colon Smooth Muscle	Colon
2	chr3:100505200-100558200	Weak transcription	Ovary	ovary
3	chr3:100505200-100582800	Weak transcription	Fetal Muscle Trunk	muscle
4	chr3:100506000-100548400	Weak transcription	Stomach Smooth Muscle	stomach
5	chr3:100514200-100547600	Weak transcription	Fetal Muscle Leg	muscle
6	chr3:100516000-100572200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr3:100517400-100594400	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr3:100518800-100543000	Weak transcription	Fetal Stomach	stomach
9	chr3:100519600-100530600	Weak transcription	Left Ventricle	heart
10	chr3:100524200-100537200	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr3:100527800-100529800	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr3:100529000-100530000	Genic enhancers	HSMM	muscle
13	chr3:100529000-100530000	Enhancers	HSMMtube	muscle
14	chr3:100529000-100530200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr3:100529000-100530200	Enhancers	NH-A	brain
16	chr3:100529000-100530400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr3:100529000-100530600	Enhancers	NHLF	lung
18	chr3:100529000-100530800	Enhancers	Osteobl	bone
19	chr3:100529000-100531600	Genic enhancers	NHDF-Ad	bronchial
20	chr3:100529200-100530000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr3:100529200-100530200	Enhancers	Muscle Satellite Cultured Cells	--
22	chr3:100529200-100530800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr3:100529400-100530000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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