Variant report

Variant	rs12496951
Chromosome Location	chr3:100516319-100516320
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11716316	0.95[CHB][hapmap];0.84[CHD][hapmap];0.85[ASN][1000 genomes]
rs1394077	0.88[YRI][hapmap]
rs1503839	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1503845	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16842822	0.87[CHD][hapmap]
rs16842845	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1847391	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs34281646	0.95[ASN][1000 genomes]
rs35734168	0.85[ASN][1000 genomes]
rs3736534	0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs3862285	0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs4616685	0.91[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs544500	0.95[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs547330	0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs58758917	0.87[ASN][1000 genomes]
rs6775161	0.81[CEU][hapmap]
rs754462	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs7609779	0.84[CHD][hapmap];0.82[JPT][hapmap];0.85[YRI][hapmap]
rs7612334	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7613610	0.90[CHD][hapmap];0.86[JPT][hapmap]
rs7628413	0.86[GIH][hapmap]
rs7632038	0.82[ASW][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap];0.85[LWK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs7642041	0.84[GIH][hapmap]
rs7642942	0.90[CHD][hapmap]
rs764684	0.88[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9824346	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs983474	0.82[JPT][hapmap]
rs9840549	0.85[CEU][hapmap];0.83[YRI][hapmap]
rs9842968	0.84[CHD][hapmap];0.82[JPT][hapmap]
rs9850273	0.90[CHD][hapmap];0.86[JPT][hapmap]
rs9879088	0.82[TSI][hapmap];0.92[YRI][hapmap]
rs989793	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs989794	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs989795	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[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	esv1796184	chr3:100507827-100522384	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
2	nsv591170	chr3:100514481-100522220	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
3	esv1795329	chr3:100514481-100522384	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
4	esv1803695	chr3:100514481-100522384	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12496951	ST3GAL6	cis	parietal	SCAN
rs12496951	TFG	cis	multi-tissue	Pritchard
rs12496951	TFG	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100475600-100520000	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr3:100494800-100523400	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr3:100501200-100516600	Weak transcription	HSMM	muscle
4	chr3:100502200-100518600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr3:100502400-100530400	Weak transcription	Colon Smooth Muscle	Colon
6	chr3:100502600-100516800	Weak transcription	Rectal Smooth Muscle	rectum
7	chr3:100505000-100516600	Weak transcription	Left Ventricle	heart
8	chr3:100505200-100558200	Weak transcription	Ovary	ovary
9	chr3:100505200-100582800	Weak transcription	Fetal Muscle Trunk	muscle
10	chr3:100506000-100548400	Weak transcription	Stomach Smooth Muscle	stomach
11	chr3:100509200-100518200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr3:100513600-100523000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr3:100514200-100547600	Weak transcription	Fetal Muscle Leg	muscle
14	chr3:100514400-100529000	Weak transcription	HSMMtube	muscle
15	chr3:100515200-100518800	Enhancers	Fetal Stomach	stomach
16	chr3:100515400-100516400	Enhancers	Muscle Satellite Cultured Cells	--
17	chr3:100515400-100517200	Enhancers	Fetal Lung	lung
18	chr3:100515400-100521800	Enhancers	NHDF-Ad	bronchial
19	chr3:100515600-100519200	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr3:100515600-100522600	Weak transcription	Osteobl	bone
21	chr3:100515800-100517400	Enhancers	Duodenum Smooth Muscle	Duodenum
22	chr3:100516000-100516600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr3:100516000-100523000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr3:100516000-100572200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr3:100516200-100516600	Weak transcription	HUVEC	blood vessel

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