Variant report

Variant	rs1879797
Chromosome Location	chr3:160395093-160395094
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10936207	0.86[ASN][1000 genomes]
rs10936208	0.85[ASN][1000 genomes]
rs10936209	0.86[ASN][1000 genomes]
rs10936210	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11714916	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11927913	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12490985	0.81[ASN][1000 genomes]
rs12639488	0.87[CEU][hapmap]
rs13095931	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1317085	0.86[ASN][1000 genomes]
rs1403045	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1522285	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16831337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17236586	0.91[CEU][hapmap];0.89[CHB][hapmap];0.80[JPT][hapmap];0.86[ASN][1000 genomes]
rs1882125	0.87[CEU][hapmap]
rs1980277	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2178452	0.86[ASN][1000 genomes]
rs2367209	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28544045	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs28730907	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs34362576	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs34949451	0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs35308461	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs35480231	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs35498840	0.87[CEU][hapmap]
rs35664264	0.86[ASN][1000 genomes]
rs35867836	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs36118017	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4133253	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4679659	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4679660	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4679909	0.83[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.86[ASN][1000 genomes]
rs62272216	0.86[ASN][1000 genomes]
rs62272217	0.86[ASN][1000 genomes]
rs62272218	0.86[ASN][1000 genomes]
rs62272219	0.80[ASN][1000 genomes]
rs62272220	0.89[ASN][1000 genomes]
rs6773389	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6774379	0.86[ASN][1000 genomes]
rs6774566	0.86[ASN][1000 genomes]
rs6776873	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6777739	0.88[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs6779581	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6779671	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6787452	0.86[ASN][1000 genomes]
rs6797760	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6798462	0.91[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs6801373	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6801636	0.80[AMR][1000 genomes]
rs6803670	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6806755	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7610939	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7633839	0.87[CEU][hapmap]
rs7634255	0.87[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv877703	chr3:160325458-160398885	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1879797	SMC4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160389400-160395200	Weak transcription	Pancreas	Pancrea
2	chr3:160389400-160395400	Weak transcription	Small Intestine	intestine
3	chr3:160391400-160395200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr3:160392000-160395200	Weak transcription	HepG2	liver
5	chr3:160393400-160395200	Enhancers	Fetal Intestine Large	intestine
6	chr3:160393400-160395800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr3:160393400-160395800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr3:160393400-160397000	Enhancers	HMEC	breast
9	chr3:160393400-160397200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr3:160393400-160397400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr3:160393600-160395200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr3:160394000-160395200	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr3:160394200-160397400	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr3:160394400-160395200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr3:160394400-160396800	Enhancers	HUVEC	blood vessel
16	chr3:160394400-160397400	Active TSS	Stomach Mucosa	stomach
17	chr3:160394600-160395200	Enhancers	Muscle Satellite Cultured Cells	--
18	chr3:160394600-160395600	Flanking Active TSS	Hela-S3	cervix
19	chr3:160394600-160396200	Flanking Active TSS	A549	lung
20	chr3:160394600-160397400	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr3:160394800-160395200	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr3:160394800-160395200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr3:160394800-160395400	Enhancers	HSMMtube	muscle
24	chr3:160394800-160395600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr3:160394800-160395600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr3:160394800-160395600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr3:160394800-160395600	Enhancers	NHDF-Ad	bronchial
28	chr3:160394800-160395600	Enhancers	Osteobl	bone
29	chr3:160394800-160395800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr3:160394800-160396400	Enhancers	Fetal Kidney	kidney
31	chr3:160394800-160396400	Enhancers	NHLF	lung
32	chr3:160394800-160396600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr3:160394800-160396600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr3:160394800-160397800	Active TSS	Rectal Mucosa Donor 29	rectum
35	chr3:160395000-160395200	Active TSS	Fetal Stomach	stomach
36	chr3:160395000-160395400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr3:160395000-160395600	Flanking Active TSS	NHEK	skin
38	chr3:160395000-160395800	Flanking Active TSS	Fetal Intestine Small	intestine
39	chr3:160395000-160395800	Active TSS	Sigmoid Colon	Sigmoid Colon
40	chr3:160395000-160395800	Flanking Active TSS	NH-A	brain
41	chr3:160395000-160396600	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr3:160395000-160396600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr3:160395000-160397200	Active TSS	Duodenum Smooth Muscle	Duodenum
44	chr3:160395000-160397400	Active TSS	Colonic Mucosa	Colon
45	chr3:160395000-160397600	Active TSS	Rectal Mucosa Donor 31	rectum
46	chr3:160395000-160398000	Active TSS	Duodenum Mucosa	Duodenum

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