Variant report

Variant	rs12645079
Chromosome Location	chr4:120194512-120194513
allele	C/T
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]
rs10518301	0.93[CHD][hapmap]
rs11935130	0.93[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12644283	0.85[CEU][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.85[MKK][hapmap]
rs12645965	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12647635	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12649811	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12650267	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17049968	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17642800	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1858285	0.93[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs2102541	0.86[CHD][hapmap];0.84[GIH][hapmap];0.85[MKK][hapmap]
rs28421394	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28848291	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28864107	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35372126	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4833614	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4834762	0.83[CEU][hapmap];0.83[CHB][hapmap]
rs4834768	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4834769	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55732167	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56072232	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56344202	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62328369	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62328371	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62328372	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62328373	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62328374	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62328376	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62328377	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62328379	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62328398	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62328407	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62328426	0.82[ASN][1000 genomes]
rs7668423	0.83[TSI][hapmap]

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	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv948802	chr4:119844269-120208926	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv1012868	chr4:120014630-120464880	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv537232	chr4:120014630-120464880	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12645079	FABP2	cis	Heart Left Ventricle	GTEx
rs12645079	FABP2	cis	cerebellum	SCAN
rs12645079	FABP2	cis	Whole Blood	GTEx

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120135000-120195800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr4:120135400-120194600	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr4:120136200-120219200	Weak transcription	Brain Angular Gyrus	brain
4	chr4:120148200-120213600	Weak transcription	Fetal Muscle Leg	muscle
5	chr4:120159400-120200800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr4:120159400-120201600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr4:120159400-120206200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr4:120159600-120200800	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr4:120160800-120195000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr4:120166000-120195200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr4:120166400-120206200	Weak transcription	Small Intestine	intestine
12	chr4:120170600-120206200	Weak transcription	Brain Cingulate Gyrus	brain
13	chr4:120173400-120195200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr4:120174400-120206200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr4:120175600-120195200	Strong transcription	Rectal Mucosa Donor 31	rectum
16	chr4:120176800-120200800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr4:120176800-120202600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr4:120177000-120194800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr4:120177000-120195000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr4:120177000-120205600	Weak transcription	Aorta	Aorta
21	chr4:120177000-120206000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr4:120177000-120213600	Weak transcription	Lung	lung
23	chr4:120177000-120220200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr4:120177000-120220200	Weak transcription	Pancreas	Pancrea
25	chr4:120177200-120206200	Weak transcription	Colon Smooth Muscle	Colon
26	chr4:120177200-120213600	Weak transcription	Esophagus	oesophagus
27	chr4:120177800-120211400	Weak transcription	HepG2	liver
28	chr4:120178200-120213400	Weak transcription	Primary B cells from peripheral blood	blood
29	chr4:120178200-120213600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr4:120178200-120213800	Weak transcription	Primary B cells from cord blood	blood
31	chr4:120178600-120206200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr4:120178600-120217600	Weak transcription	Fetal Stomach	stomach
33	chr4:120179400-120194600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr4:120179600-120200800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr4:120180400-120200800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr4:120184000-120205200	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr4:120185800-120194800	Strong transcription	HSMM	muscle
38	chr4:120185800-120195200	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr4:120186000-120195000	Strong transcription	Fetal Intestine Large	intestine
40	chr4:120186800-120194800	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr4:120187000-120195200	Strong transcription	Liver	Liver
42	chr4:120187000-120219200	Weak transcription	Right Ventricle	heart
43	chr4:120187400-120194600	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr4:120187600-120198800	Weak transcription	Fetal Heart	heart
45	chr4:120187800-120206000	Weak transcription	Rectal Smooth Muscle	rectum
46	chr4:120188200-120195200	Weak transcription	NHLF	lung
47	chr4:120189800-120195200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr4:120189800-120206200	Weak transcription	Brain Substantia Nigra	brain
49	chr4:120190000-120194800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr4:120190000-120206000	Weak transcription	Fetal Kidney	kidney

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