Variant report

Variant	rs12649811
Chromosome Location	chr4:120183939-120183940
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:120183141..120184141-chr8:43096226..43096751,3	MCF-7	breast:
2	chr4:120183641..120184141-chr8:43096068..43096724,2	MCF-7	breast:
3	chr4:120183161..120184141-chr8:43095223..43095920,2	MCF-7	breast:
4	chr4:120183641..120184141-chr8:43094991..43095897,2	MCF-7	breast:
5	chr21:28250452..28251450-chr4:120183161..120184161,2	MCF-7	breast:
6	chr4:120182924..120185910-chr4:120187445..120191655,4	K562	blood:
7	chr4:120162306..120165092-chr4:120183039..120184970,2	K562	blood:

Variant related genes	Relation type
ENSG00000145390	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11935130	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12645079	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12645965	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12647635	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12650267	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17049968	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17642800	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1858285	0.85[ASN][1000 genomes]
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	0.90[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]
rs4834768	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4834769	0.80[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	0.84[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	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62328398	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62328407	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62328426	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12649811	FABP2	cis	Heart Left Ventricle	GTEx
rs12649811	FABP2	cis	Whole Blood	GTEx

Chromatin state (count:107 , 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	chr4:120141000-120192400	Weak transcription	Hela-S3	cervix
5	chr4:120148200-120213600	Weak transcription	Fetal Muscle Leg	muscle
6	chr4:120155600-120186000	Weak transcription	Fetal Heart	heart
7	chr4:120159400-120200800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr4:120159400-120201600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr4:120159400-120206200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr4:120159600-120200800	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr4:120159800-120188400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr4:120160800-120195000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr4:120165800-120187000	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr4:120166000-120195200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr4:120166400-120187200	Weak transcription	Fetal Kidney	kidney
16	chr4:120166400-120189800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr4:120166400-120206200	Weak transcription	Small Intestine	intestine
18	chr4:120167000-120184000	Strong transcription	Liver	Liver
19	chr4:120167000-120194400	Weak transcription	Fetal Muscle Trunk	muscle
20	chr4:120167800-120192400	Weak transcription	Psoas Muscle	Psoas
21	chr4:120170600-120185600	Weak transcription	Stomach Mucosa	stomach
22	chr4:120170600-120192600	Weak transcription	Fetal Thymus	thymus
23	chr4:120170600-120206200	Weak transcription	Brain Cingulate Gyrus	brain
24	chr4:120173400-120195200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr4:120174200-120191800	Weak transcription	Fetal Lung	lung
26	chr4:120174200-120192600	Weak transcription	Brain Anterior Caudate	brain
27	chr4:120174400-120191600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr4:120174400-120206200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr4:120175400-120189400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr4:120175600-120184000	Strong transcription	Adipose Nuclei	Adipose
31	chr4:120175600-120195200	Strong transcription	Rectal Mucosa Donor 31	rectum
32	chr4:120176000-120186000	Weak transcription	Brain Hippocampus Middle	brain
33	chr4:120176000-120186800	Weak transcription	Primary hematopoietic stem cells	blood
34	chr4:120176400-120184400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr4:120176800-120192200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr4:120176800-120193400	Strong transcription	NHDF-Ad	bronchial
37	chr4:120176800-120194400	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr4:120176800-120200800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr4:120176800-120202600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr4:120177000-120191600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr4:120177000-120192600	Weak transcription	Gastric	stomach
42	chr4:120177000-120194800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr4:120177000-120195000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr4:120177000-120205600	Weak transcription	Aorta	Aorta
45	chr4:120177000-120206000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr4:120177000-120213600	Weak transcription	Lung	lung
47	chr4:120177000-120220200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr4:120177000-120220200	Weak transcription	Pancreas	Pancrea
49	chr4:120177200-120189400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr4:120177200-120206200	Weak transcription	Colon Smooth Muscle	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links