Variant report

Variant	rs17642800
Chromosome Location	chr4:120219534-120219535
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:120218971..120221940-chr4:120223972..120225739,2	MCF-7	breast:
2	chr4:120133055..120136111-chr4:120217896..120220637,3	MCF-7	breast:
3	chr4:120130951..120136158-chr4:120218006..120223072,8	K562	blood:
4	chr4:120216851..120219563-chr4:120219999..120222854,2	K562	blood:
5	chr4:120210891..120213027-chr4:120219123..120221721,2	K562	blood:
6	chr4:119899594..119901256-chr4:120219092..120221109,2	MCF-7	breast:
7	chr4:119919801..119922456-chr4:120217871..120220047,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145390	Chromatin interaction
ENSG00000164096	Chromatin interaction
ENSG00000178636	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11935130	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12645079	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12645965	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12647635	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12649811	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12650267	0.98[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17049968	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1858285	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28421394	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28848291	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28864107	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35372126	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3905917	0.82[ASN][1000 genomes]
rs4833614	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4834768	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4834769	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4834773	0.82[ASN][1000 genomes]
rs55732167	0.81[AMR][1000 genomes]
rs56072232	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56344202	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62328369	0.85[AMR][1000 genomes]
rs62328371	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62328372	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62328373	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62328374	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62328376	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62328377	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62328379	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62328398	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62328407	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62328426	0.88[ASN][1000 genomes]
rs7681328	0.81[ASN][1000 genomes]

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	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
3	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
4	nsv428769	chr4:120205572-120363323	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17642800	FABP2	cis	Heart Left Ventricle	GTEx
rs17642800	FABP2	cis	Whole Blood	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120177000-120220200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:120177000-120220200	Weak transcription	Pancreas	Pancrea
3	chr4:120201200-120220200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr4:120201200-120220200	Weak transcription	Gastric	stomach
5	chr4:120201400-120220200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr4:120202000-120220200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr4:120206400-120219600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr4:120206400-120219800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr4:120206400-120219800	Weak transcription	Brain Substantia Nigra	brain
10	chr4:120206400-120220000	Weak transcription	Colonic Mucosa	Colon
11	chr4:120206600-120219600	Weak transcription	Brain Hippocampus Middle	brain
12	chr4:120206600-120219800	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr4:120206600-120220200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr4:120206800-120220200	Weak transcription	Stomach Mucosa	stomach
15	chr4:120207600-120219800	Weak transcription	Rectal Smooth Muscle	rectum
16	chr4:120214400-120220000	Weak transcription	Thymus	Thymus
17	chr4:120214400-120220200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr4:120214400-120220200	Weak transcription	Esophagus	oesophagus
19	chr4:120214400-120220200	Weak transcription	Lung	lung
20	chr4:120216600-120219600	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr4:120216600-120219800	Strong transcription	Primary B cells from peripheral blood	blood
22	chr4:120216800-120219800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr4:120217000-120219800	Strong transcription	Fetal Thymus	thymus
24	chr4:120217000-120220200	Weak transcription	Spleen	Spleen
25	chr4:120217400-120219800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr4:120217400-120219800	Strong transcription	Fetal Lung	lung
27	chr4:120217400-120219800	Strong transcription	HSMM	muscle
28	chr4:120217800-120219800	Strong transcription	K562	blood
29	chr4:120217800-120220000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
30	chr4:120218000-120219600	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr4:120218000-120219800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr4:120218200-120219800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr4:120218200-120220000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr4:120218200-120220000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr4:120218200-120220200	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr4:120218400-120219800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr4:120218400-120219800	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr4:120218400-120220000	Weak transcription	Fetal Kidney	kidney
39	chr4:120218400-120220000	Weak transcription	Psoas Muscle	Psoas
40	chr4:120218400-120220200	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr4:120218400-120220400	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr4:120218400-120220600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr4:120218600-120219600	Strong transcription	Cortex derived primary cultured neurospheres	brain
44	chr4:120218600-120219600	Weak transcription	Brain Cingulate Gyrus	brain
45	chr4:120218600-120219800	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr4:120218600-120220000	Weak transcription	Brain Germinal Matrix	brain
47	chr4:120218600-120220200	Weak transcription	Fetal Brain Female	brain
48	chr4:120218800-120219600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr4:120218800-120220000	Weak transcription	Left Ventricle	heart
50	chr4:120219000-120219600	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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