Variant report

Variant	rs6556937
Chromosome Location	chr5:95985282-95985283
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:95985044..95987422-chr5:95998320..96000663,2	MCF-7	breast:
2	chr5:95976037..95979831-chr5:95983868..95989174,6	MCF-7	breast:
3	chr5:95984144..95985957-chr5:95992996..95994996,2	K562	blood:
4	chr5:95982894..95985844-chr5:95986836..95989729,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000153113	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10045215	0.91[ASN][1000 genomes]
rs10067766	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10075736	0.91[ASN][1000 genomes]
rs1421911	0.90[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs151835	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs151904	1.00[JPT][hapmap]
rs152005	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs152014	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs152017	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs152020	0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2351245	0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs26482	0.89[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs26483	0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs26484	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs26485	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs26503	1.00[JPT][hapmap]
rs26504	1.00[JPT][hapmap]
rs28040	0.81[ASN][1000 genomes]
rs28093	0.86[JPT][hapmap]
rs28104	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs31248	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs31249	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs31250	0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4267886	0.87[ASN][1000 genomes]
rs4590196	0.88[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6860934	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6897588	0.90[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7704167	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7705824	0.85[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7733671	0.89[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.85[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	nsv1030444	chr5:95353620-95995619	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
2	nsv537810	chr5:95353620-95995619	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
3	nsv1024964	chr5:95742124-96065492	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv537811	chr5:95742124-96065492	Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs6556937	CAST	cis	cerebellum	SCAN
rs6556937	TBX4	trans	parietal	SCAN
rs6556937	CAST	cis	Nerve Tibial	GTEx
rs6556937	CAST	cis	Whole Blood	GTEx
rs6556937	CAST	cis	parietal	SCAN
rs6556937	CTC-506B8.1	cis	Whole Blood	GTEx
rs6556937	CAST	cis	lung	GTEx
rs6556937	CAST	cis	multi-tissue	Pritchard
rs6556937	CAST	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:95980800-95988200	Weak transcription	Placenta	Placenta
2	chr5:95982800-95986200	Enhancers	Skeletal Muscle Female	skeletal muscle
3	chr5:95982800-95989600	Enhancers	Monocytes-CD14+_RO01746	blood
4	chr5:95983200-95986400	Enhancers	Rectal Mucosa Donor 29	rectum
5	chr5:95983200-95986600	Enhancers	Fetal Intestine Large	intestine
6	chr5:95983200-95994200	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr5:95983400-95985400	Enhancers	Skeletal Muscle Male	skeletal muscle
8	chr5:95983400-95985600	Enhancers	Sigmoid Colon	Sigmoid Colon
9	chr5:95983400-95986200	Enhancers	Primary neutrophils fromperipheralblood	blood
10	chr5:95983400-95986200	Enhancers	Fetal Lung	lung
11	chr5:95983400-95986400	Enhancers	Rectal Mucosa Donor 31	rectum
12	chr5:95983600-95985600	Enhancers	A549	lung
13	chr5:95983600-95986200	Enhancers	Fetal Intestine Small	intestine
14	chr5:95983800-95986000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr5:95983800-95986000	Enhancers	Liver	Liver
16	chr5:95983800-95986000	Enhancers	HMEC	breast
17	chr5:95983800-95986200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr5:95983800-95990800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr5:95984400-95985800	Enhancers	HepG2	liver
20	chr5:95984400-95986000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr5:95984400-95986000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr5:95984400-95986000	Enhancers	Adipose Nuclei	Adipose
23	chr5:95984400-95986000	Enhancers	Stomach Mucosa	stomach
24	chr5:95984400-95986200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr5:95984400-95986200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr5:95984400-95986200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr5:95984400-95986200	Enhancers	Brain Inferior Temporal Lobe	brain
28	chr5:95984400-95986200	Enhancers	Hela-S3	cervix
29	chr5:95984400-95986400	Enhancers	Brain Substantia Nigra	brain
30	chr5:95984400-95986600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr5:95984400-95986800	Enhancers	Brain Anterior Caudate	brain
32	chr5:95984400-95987200	Enhancers	Fetal Kidney	kidney
33	chr5:95984400-95987400	Enhancers	Brain Cingulate Gyrus	brain
34	chr5:95984400-95987400	Enhancers	Brain Hippocampus Middle	brain
35	chr5:95984400-95987600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr5:95984400-95989200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr5:95984600-95986200	Enhancers	NHEK	skin
38	chr5:95984600-95986200	Enhancers	NHLF	lung
39	chr5:95984600-95988200	Weak transcription	Esophagus	oesophagus
40	chr5:95984800-95985400	Weak transcription	Brain Angular Gyrus	brain
41	chr5:95984800-95986600	Weak transcription	GM12878-XiMat	blood
42	chr5:95984800-95986600	Enhancers	NHDF-Ad	bronchial
43	chr5:95984800-95989400	Enhancers	Placenta Amnion	Placenta Amnion
44	chr5:95984800-95991000	Weak transcription	Psoas Muscle	Psoas
45	chr5:95984800-95991400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr5:95985200-95985400	Enhancers	Pancreas	Pancrea
47	chr5:95985200-95986000	Enhancers	Osteobl	bone
48	chr5:95985200-95987200	Weak transcription	Small Intestine	intestine
49	chr5:95985200-95988400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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