Variant report

Variant	rs2713758
Chromosome Location	chr3:100711583-100711584
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs13085823	0.83[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs1375512	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1449299	0.95[ASN][1000 genomes]
rs1530731	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1579969	0.83[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs16843153	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17339226	1.00[CEU][hapmap];0.86[CHB][hapmap];0.96[GIH][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17340282	0.85[ASN][1000 genomes]
rs1836985	0.86[CHB][hapmap]
rs2595907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs2713749	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2713798	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];0.84[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs55687619	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55936420	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56077494	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56237429	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59476872	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6774218	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6787197	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6787878	0.90[CEU][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73141447	0.85[ASN][1000 genomes]
rs73143038	0.80[EUR][1000 genomes]
rs73143044	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73143061	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73143062	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73143064	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73143072	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73144908	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73144910	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73144915	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73144970	0.95[ASN][1000 genomes]
rs73149160	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73149173	0.80[ASN][1000 genomes]
rs7621518	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7623956	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7625454	1.00[CEU][hapmap];0.86[CHB][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7637274	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7641631	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7643050	0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs959713	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931417	chr3:100547347-101183844	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	esv2757881	chr3:100613387-100776497	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	esv2759163	chr3:100613387-100776497	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2713758	ST3GAL6	cis	cerebellum	SCAN
rs2713758	ABI3BP	cis	parietal	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100709000-100712600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr3:100709200-100713000	Active TSS	Stomach Smooth Muscle	stomach
3	chr3:100709600-100711600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr3:100709600-100712400	Active TSS	HSMMtube	muscle
5	chr3:100709800-100711600	Active TSS	Osteobl	bone
6	chr3:100709800-100712400	Active TSS	Fetal Muscle Leg	muscle
7	chr3:100709800-100712400	Active TSS	NHDF-Ad	bronchial
8	chr3:100709800-100712600	Active TSS	Muscle Satellite Cultured Cells	--
9	chr3:100709800-100712600	Active TSS	Fetal Stomach	stomach
10	chr3:100710000-100712800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr3:100710000-100712800	Active TSS	Fetal Lung	lung
12	chr3:100710200-100712200	Active TSS	Right Atrium	heart
13	chr3:100710200-100712400	Active TSS	Duodenum Smooth Muscle	Duodenum
14	chr3:100710200-100712600	Active TSS	Fetal Muscle Trunk	muscle
15	chr3:100710400-100712400	Active TSS	Colon Smooth Muscle	Colon
16	chr3:100710400-100712400	Active TSS	NHLF	lung
17	chr3:100710400-100712800	Active TSS	Rectal Smooth Muscle	rectum
18	chr3:100710600-100711600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr3:100710600-100712400	Active TSS	Ovary	ovary
20	chr3:100710600-100712400	Active TSS	Rectal Mucosa Donor 29	rectum
21	chr3:100710600-100712600	Active TSS	Fetal Intestine Large	intestine
22	chr3:100710800-100711600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr3:100710800-100711800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr3:100710800-100711800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
25	chr3:100710800-100712200	Active TSS	Duodenum Mucosa	Duodenum
26	chr3:100710800-100712400	Active TSS	Fetal Intestine Small	intestine
27	chr3:100710800-100712400	Active TSS	Skeletal Muscle Female	skeletal muscle
28	chr3:100711000-100711600	Active TSS	Breast Myoepithelial Primary Cells	Breast
29	chr3:100711000-100711600	Active TSS	HSMM	muscle
30	chr3:100711000-100711800	ZNF genes & repeats	Fetal Brain Male	brain
31	chr3:100711000-100711800	Active TSS	Skeletal Muscle Male	skeletal muscle
32	chr3:100711000-100712000	Active TSS	Brain Hippocampus Middle	brain
33	chr3:100711000-100712000	Active TSS	Stomach Mucosa	stomach
34	chr3:100711000-100712000	Flanking Active TSS	A549	lung
35	chr3:100711000-100712200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr3:100711000-100712200	Active TSS	Pancreatic Islets	Pancreatic Islet
37	chr3:100711000-100712200	Active TSS	Left Ventricle	heart
38	chr3:100711000-100712400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr3:100711000-100712400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr3:100711000-100712400	Active TSS	Aorta	Aorta
41	chr3:100711000-100712400	Active TSS	Brain Anterior Caudate	brain
42	chr3:100711000-100712400	Active TSS	Brain Substantia Nigra	brain
43	chr3:100711000-100712400	Active TSS	Colonic Mucosa	Colon
44	chr3:100711000-100712400	Active TSS	Psoas Muscle	Psoas
45	chr3:100711000-100712400	Flanking Active TSS	NHEK	skin
46	chr3:100711200-100711600	Flanking Active TSS	Liver	Liver
47	chr3:100711200-100711800	Active TSS	Brain Germinal Matrix	brain
48	chr3:100711200-100711800	Active TSS	Lung	lung
49	chr3:100711200-100712000	Flanking Active TSS	Fetal Kidney	kidney
50	chr3:100711200-100712000	Enhancers	HepG2	liver

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