Variant report

Variant	rs10499181
Chromosome Location	chr6:131325520-131325521
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	STAT3	chr6:131325496-131325622	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
EPB41L2	TF binding region

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10499175	0.82[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes]
rs10499176	1.00[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap];1.00[AFR][1000 genomes]
rs10499178	1.00[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs17053471	1.00[AFR][1000 genomes]
rs17059726	1.00[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap]
rs17059735	1.00[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes]
rs17059739	1.00[CEU][hapmap];0.82[CHB][hapmap];0.83[JPT][hapmap];1.00[AFR][1000 genomes]
rs17059760	1.00[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes]
rs17059787	1.00[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17059799	1.00[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17059801	1.00[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17059808	1.00[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes]
rs17059810	1.00[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17059851	1.00[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs17059853	1.00[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs17059909	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs17059938	0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs17059963	1.00[CEU][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs17059968	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs17059974	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs17059981	0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs17060041	1.00[AFR][1000 genomes]
rs1972244	1.00[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1999473	1.00[CEU][hapmap];0.88[CHB][hapmap];0.93[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2183968	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2275064	1.00[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes]
rs2839942	0.82[CHB][hapmap]
rs3777433	1.00[CEU][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes]
rs3777437	1.00[AFR][1000 genomes]
rs3777443	1.00[AFR][1000 genomes]
rs3777444	1.00[CEU][hapmap]
rs3777447	1.00[AFR][1000 genomes]
rs3777448	1.00[CEU][hapmap];0.87[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3777451	1.00[CEU][hapmap];0.82[CHB][hapmap];0.83[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3777456	1.00[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3822859	1.00[CEU][hapmap];0.82[CHB][hapmap];0.83[JPT][hapmap];1.00[AFR][1000 genomes]
rs3822860	0.82[CHB][hapmap];0.83[JPT][hapmap];1.00[AFR][1000 genomes]
rs3822865	0.82[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs41285328	1.00[AMR][1000 genomes]
rs41311408	1.00[AMR][1000 genomes]
rs4142572	1.00[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs4142581	0.81[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs45577234	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs57189640	1.00[AFR][1000 genomes]
rs57208456	1.00[AFR][1000 genomes]
rs57211621	1.00[AFR][1000 genomes]
rs58130017	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs59036192	1.00[AFR][1000 genomes]
rs59271461	0.86[ASN][1000 genomes]
rs59627131	1.00[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs60215702	1.00[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs60697593	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs60732147	1.00[AFR][1000 genomes]
rs60877807	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs60954662	1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs61217522	1.00[AFR][1000 genomes]
rs61625259	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs714709	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs72499769	1.00[AFR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:131315800-131325800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:131318800-131325800	Weak transcription	Fetal Thymus	thymus
3	chr6:131318800-131328000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr6:131318800-131329200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr6:131319000-131325600	Weak transcription	Rectal Smooth Muscle	rectum
6	chr6:131321000-131326600	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr6:131321400-131325600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr6:131321800-131327200	Enhancers	Fetal Stomach	stomach
9	chr6:131322000-131325600	Weak transcription	Stomach Mucosa	stomach
10	chr6:131322400-131325800	Weak transcription	Placenta	Placenta
11	chr6:131322400-131327000	Enhancers	Brain Substantia Nigra	brain
12	chr6:131322600-131326600	Enhancers	Brain Hippocampus Middle	brain
13	chr6:131322600-131326800	Enhancers	Brain Cingulate Gyrus	brain
14	chr6:131322600-131327000	Enhancers	Brain Anterior Caudate	brain
15	chr6:131322600-131327000	Enhancers	Fetal Lung	lung
16	chr6:131322600-131333200	Weak transcription	Pancreas	Pancrea
17	chr6:131323000-131325600	Enhancers	Adipose Nuclei	Adipose
18	chr6:131323200-131326000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr6:131323400-131325600	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr6:131323600-131325600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr6:131323600-131325600	Weak transcription	Duodenum Mucosa	Duodenum
22	chr6:131323600-131325600	Weak transcription	Spleen	Spleen
23	chr6:131323600-131326600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr6:131323600-131327000	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr6:131323600-131327800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr6:131323600-131328200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr6:131323800-131325800	Weak transcription	NHDF-Ad	bronchial
28	chr6:131323800-131326000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr6:131323800-131327000	Enhancers	NHLF	lung
30	chr6:131323800-131328000	Weak transcription	A549	lung
31	chr6:131323800-131328200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr6:131324000-131334200	Weak transcription	Small Intestine	intestine
33	chr6:131324200-131326800	Enhancers	Fetal Heart	heart
34	chr6:131324400-131325800	Enhancers	iPS-18 Cell Line	embryonic stem cell
35	chr6:131324400-131325800	Enhancers	HSMM	muscle
36	chr6:131324400-131326000	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr6:131324400-131326800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr6:131324600-131326000	Enhancers	ES-I3 Cell Line	embryonic stem cell
39	chr6:131324600-131326000	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr6:131324600-131326000	Enhancers	Fetal Kidney	kidney
41	chr6:131324600-131326000	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr6:131324600-131326400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
43	chr6:131324600-131327200	Enhancers	Fetal Muscle Leg	muscle
44	chr6:131324600-131327400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr6:131324800-131326200	Enhancers	H1 Cell Line	embryonic stem cell
46	chr6:131324800-131326200	Enhancers	iPS-20b Cell Line	embryonic stem cell
47	chr6:131324800-131328000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr6:131325000-131325800	Enhancers	Colon Smooth Muscle	Colon
49	chr6:131325000-131326000	Enhancers	H9 Cell Line	embryonic stem cell
50	chr6:131325000-131326000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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