Variant report

Variant	rs62328373
Chromosome Location	chr4:120167453-120167454
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:120131927..120134724-chr4:120165743..120168558,4	K562	blood:
2	chr4:120132009..120134724-chr4:120165743..120167609,3	K562	blood:
3	chr4:120131912..120135684-chr4:120163783..120168921,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000178636	Chromatin interaction
ENSG00000145390	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11935130	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12645079	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12645965	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12647635	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12649811	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12650267	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17049968	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17642800	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1858285	0.84[ASN][1000 genomes]
rs28421394	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28848291	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28864107	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35372126	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4833614	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4834768	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4834769	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55732167	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56072232	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56344202	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62328369	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62328371	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62328372	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62328374	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62328376	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62328377	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62328379	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62328398	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62328407	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
5	esv2763386	chr4:120143861-120186968	Strong transcription ZNF genes & repeats Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv461632	chr4:120158734-120180790	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv461633	chr4:120158734-120180790	Strong transcription Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv595332	chr4:120158734-120180790	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs62328373	FABP2	cis	Whole Blood	GTEx
rs62328373	FABP2	cis	Heart Left Ventricle	GTEx

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120134800-120170000	Weak transcription	Colon Smooth Muscle	Colon
2	chr4:120135000-120170400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:120135000-120195800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr4:120135200-120176200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr4:120135200-120176200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr4:120135400-120194600	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr4:120135600-120173800	Weak transcription	Brain Anterior Caudate	brain
8	chr4:120136200-120219200	Weak transcription	Brain Angular Gyrus	brain
9	chr4:120141000-120192400	Weak transcription	Hela-S3	cervix
10	chr4:120143000-120176200	Weak transcription	Esophagus	oesophagus
11	chr4:120146000-120178600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr4:120148200-120213600	Weak transcription	Fetal Muscle Leg	muscle
13	chr4:120155400-120169800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr4:120155400-120169800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr4:120155400-120169800	Weak transcription	Ovary	ovary
16	chr4:120155400-120176200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr4:120155400-120176400	Weak transcription	Right Ventricle	heart
18	chr4:120155600-120169800	Weak transcription	Rectal Smooth Muscle	rectum
19	chr4:120155600-120173800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr4:120155600-120176400	Weak transcription	Brain Substantia Nigra	brain
21	chr4:120155600-120186000	Weak transcription	Fetal Heart	heart
22	chr4:120157000-120170000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr4:120157600-120176800	Weak transcription	Primary B cells from cord blood	blood
24	chr4:120159400-120200800	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr4:120159400-120201600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr4:120159400-120206200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr4:120159600-120170000	Weak transcription	K562	blood
28	chr4:120159600-120200800	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr4:120159800-120188400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr4:120160400-120174200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr4:120160800-120195000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr4:120161000-120173800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr4:120161600-120170000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr4:120162400-120168000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr4:120162400-120176600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr4:120163800-120169800	Weak transcription	Brain Cingulate Gyrus	brain
37	chr4:120163800-120175600	Weak transcription	Brain Hippocampus Middle	brain
38	chr4:120164000-120176600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr4:120164600-120173000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr4:120165000-120168000	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr4:120165000-120171400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr4:120165600-120172400	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr4:120165800-120168000	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr4:120165800-120172000	Strong transcription	NHDF-Ad	bronchial
45	chr4:120165800-120179400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr4:120165800-120187000	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr4:120166000-120168800	Strong transcription	HMEC	breast
48	chr4:120166000-120183600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr4:120166000-120195200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr4:120166200-120170000	Weak transcription	Stomach Mucosa	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links