Variant report

Variant	rs1190802
Chromosome Location	chr6:131511203-131511204
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F4	chr6:131510759-131511231	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr6:131511112-131511225	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
ENSG00000218857	TF binding region

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10484763	0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10484764	0.89[JPT][hapmap]
rs1190788	1.00[CEU][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs1190794	1.00[CEU][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs1190796	0.98[EUR][1000 genomes]
rs1190799	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs1190800	0.99[EUR][1000 genomes]
rs1190801	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs1190805	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs1190806	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs1190809	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1190810	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1190812	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1209159	0.96[CEU][hapmap];0.96[EUR][1000 genomes]
rs12525492	1.00[JPT][hapmap]
rs12526166	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12660246	0.87[ASN][1000 genomes]
rs12662825	1.00[JPT][hapmap]
rs12664060	0.86[ASN][1000 genomes]
rs1322596	0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs17060099	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs17060119	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs17060127	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1729549	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs1729558	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs1746469	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1746470	0.95[EUR][1000 genomes]
rs1746471	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs1746473	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs1746474	0.95[EUR][1000 genomes]
rs2224637	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs28360555	0.81[EUR][1000 genomes]
rs3756773	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs3777469	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs3777470	0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs3777471	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs3777473	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs3777474	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777476	0.81[EUR][1000 genomes]
rs3777477	0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3777479	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs3777481	0.83[ASN][1000 genomes]
rs3777482	0.80[ASN][1000 genomes]
rs3777484	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs3777491	1.00[JPT][hapmap]
rs3777495	0.94[JPT][hapmap]
rs3777496	0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs3777497	1.00[JPT][hapmap]
rs3777498	1.00[JPT][hapmap]
rs3777499	1.00[JPT][hapmap]
rs3822867	1.00[JPT][hapmap]
rs3850239	0.80[EUR][1000 genomes]
rs4596509	0.95[ASN][1000 genomes]
rs66533103	0.82[EUR][1000 genomes]
rs9492864	0.82[EUR][1000 genomes]
rs9492865	0.86[YRI][hapmap];0.81[EUR][1000 genomes]
rs9492868	0.81[EUR][1000 genomes]
rs9492889	1.00[JPT][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	nsv1032955	chr6:131298803-131818502	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv538443	chr6:131298803-131818502	Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv830807	chr6:131390952-131581931	Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv886664	chr6:131443843-131754930	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:131457600-131520800	Weak transcription	Right Ventricle	heart
2	chr6:131458200-131513400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr6:131485600-131514000	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr6:131487000-131512800	Weak transcription	Brain Hippocampus Middle	brain
5	chr6:131488200-131534800	Weak transcription	Gastric	stomach
6	chr6:131489000-131513000	Weak transcription	Colon Smooth Muscle	Colon
7	chr6:131494800-131514000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr6:131504200-131514000	Weak transcription	Brain Germinal Matrix	brain
9	chr6:131504600-131512800	Weak transcription	Brain Angular Gyrus	brain
10	chr6:131505000-131512000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr6:131505000-131518800	Weak transcription	Thymus	Thymus
12	chr6:131505000-131521000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr6:131505000-131521800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr6:131505200-131512800	Weak transcription	Aorta	Aorta
15	chr6:131505200-131513400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr6:131505200-131522600	Weak transcription	HSMMtube	muscle
17	chr6:131505800-131534600	Weak transcription	Brain Substantia Nigra	brain
18	chr6:131505800-131534800	Weak transcription	Pancreas	Pancrea
19	chr6:131506000-131515800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr6:131506200-131512800	Weak transcription	Left Ventricle	heart
21	chr6:131506400-131512600	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr6:131506400-131512800	Weak transcription	Brain Cingulate Gyrus	brain
23	chr6:131506400-131512800	Weak transcription	Placenta	Placenta
24	chr6:131506400-131512800	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr6:131506400-131520800	Weak transcription	Duodenum Mucosa	Duodenum
26	chr6:131506600-131512800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr6:131506600-131512800	Weak transcription	Esophagus	oesophagus
28	chr6:131506600-131512800	Weak transcription	Fetal Intestine Small	intestine
29	chr6:131506600-131512800	Weak transcription	Fetal Muscle Leg	muscle
30	chr6:131506600-131512800	Weak transcription	Fetal Stomach	stomach
31	chr6:131506600-131514200	Weak transcription	Stomach Smooth Muscle	stomach
32	chr6:131506600-131520600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr6:131506600-131520600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr6:131506600-131520600	Weak transcription	Spleen	Spleen
35	chr6:131506600-131520800	Weak transcription	Lung	lung
36	chr6:131506600-131523800	Weak transcription	HepG2	liver
37	chr6:131506600-131524000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr6:131506600-131529800	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr6:131506600-131532000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr6:131506800-131512000	Weak transcription	Adipose Nuclei	Adipose
41	chr6:131506800-131512600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr6:131506800-131512600	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr6:131506800-131512800	Weak transcription	Brain Anterior Caudate	brain
44	chr6:131506800-131512800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr6:131506800-131512800	Weak transcription	Fetal Muscle Trunk	muscle
46	chr6:131506800-131514200	Weak transcription	Dnd41	blood
47	chr6:131506800-131518600	Weak transcription	Primary B cells from cord blood	blood
48	chr6:131506800-131551800	Weak transcription	Ovary	ovary
49	chr6:131507000-131520400	Weak transcription	Liver	Liver
50	chr6:131507200-131512600	Weak transcription	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links