Variant report

Variant	rs7904512
Chromosome Location	chr10:5902459-5902460
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:5853453..5856522-chr10:5901378..5904221,3	K562	blood:
2	chr10:5853575..5857221-chr10:5900529..5905112,5	MCF-7	breast:
3	chr10:5900731..5902492-chr10:5915568..5917160,2	K562	blood:

Variant related genes	Relation type
ENSG00000057608	Chromatin interaction
ENSG00000272764	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs11255581	0.82[JPT][hapmap]
rs11592964	1.00[AFR][1000 genomes]
rs11594153	1.00[AFR][1000 genomes]
rs11594794	0.82[JPT][hapmap]
rs11595457	1.00[AFR][1000 genomes]
rs11598581	0.90[EUR][1000 genomes]
rs11598865	1.00[CEU][hapmap];0.82[JPT][hapmap];0.90[EUR][1000 genomes]
rs11813102	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs12774966	0.82[JPT][hapmap]
rs17146333	1.00[CEU][hapmap];0.82[JPT][hapmap];0.87[EUR][1000 genomes]
rs17146580	1.00[CEU][hapmap];0.82[JPT][hapmap];0.80[EUR][1000 genomes]
rs17146587	1.00[CEU][hapmap];0.82[JPT][hapmap];0.80[EUR][1000 genomes]
rs17146629	1.00[CEU][hapmap];0.82[JPT][hapmap];0.80[EUR][1000 genomes]
rs2031230	1.00[CEU][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes]
rs2137422	1.00[AFR][1000 genomes]
rs2203197	0.82[JPT][hapmap]
rs2274026	1.00[CEU][hapmap];1.00[MEX][hapmap];0.83[EUR][1000 genomes]
rs2274027	0.82[JPT][hapmap]
rs2274028	1.00[CEU][hapmap];0.82[JPT][hapmap];0.87[EUR][1000 genomes]
rs2274031	1.00[CEU][hapmap];0.82[JPT][hapmap];0.80[EUR][1000 genomes]
rs2274033	1.00[CEU][hapmap];0.82[JPT][hapmap];0.80[EUR][1000 genomes]
rs2296136	1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs2296137	0.87[CEU][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.90[EUR][1000 genomes]
rs2296138	1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.90[EUR][1000 genomes]
rs2380205	0.82[JPT][hapmap]
rs2380208	0.82[JPT][hapmap]
rs34249852	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34455477	0.93[EUR][1000 genomes]
rs3750656	1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3750659	0.97[EUR][1000 genomes]
rs41290311	0.90[EUR][1000 genomes]
rs41306916	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4293038	0.82[JPT][hapmap]
rs4330991	1.00[JPT][hapmap]
rs4749325	1.00[AFR][1000 genomes]
rs4749407	1.00[AFR][1000 genomes]
rs55718140	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56103646	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56213022	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56296494	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56333805	0.90[EUR][1000 genomes]
rs56354230	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7072174	0.82[JPT][hapmap]
rs7098372	0.82[JPT][hapmap]
rs7099029	0.82[JPT][hapmap]
rs713588	0.82[JPT][hapmap]
rs7893821	1.00[CEU][hapmap];0.82[JPT][hapmap];0.80[EUR][1000 genomes]
rs7894083	0.82[JPT][hapmap]
rs7897260	0.82[JPT][hapmap]
rs7899635	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs7899847	1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.90[EUR][1000 genomes]
rs7902223	1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.90[EUR][1000 genomes]
rs7904712	1.00[CEU][hapmap];0.82[JPT][hapmap];0.87[EUR][1000 genomes]
rs7912210	1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.90[EUR][1000 genomes]
rs7918162	1.00[CEU][hapmap]
rs7923781	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs867052	0.82[JPT][hapmap]
rs907685	0.82[JPT][hapmap]
rs907688	0.82[JPT][hapmap]
rs907689	0.82[JPT][hapmap]
rs9663697	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34147	chr10:5726821-6105717	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv34061	chr10:5726821-6225187	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv1042286	chr10:5795129-6578445	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	nsv831775	chr10:5804335-6000849	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv5654	chr10:5868365-5930634	Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv825229	chr10:5886905-5967697	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv466722	chr10:5893268-5916201	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv549904	chr10:5893268-5916201	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv437655	chr10:5900973-5910361	Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:5888800-5904400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr10:5894600-5908600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr10:5894600-5908600	Weak transcription	K562	blood
4	chr10:5894600-5916800	Weak transcription	Spleen	Spleen
5	chr10:5896200-5912200	Weak transcription	Fetal Muscle Trunk	muscle
6	chr10:5896400-5918200	Weak transcription	Fetal Lung	lung
7	chr10:5896600-5903800	Weak transcription	Fetal Stomach	stomach
8	chr10:5897000-5903800	Weak transcription	Primary B cells from peripheral blood	blood
9	chr10:5899000-5904200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr10:5899200-5903000	Weak transcription	HepG2	liver
11	chr10:5899800-5904200	Weak transcription	Ovary	ovary
12	chr10:5899800-5905000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr10:5900000-5904000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr10:5900000-5916600	Weak transcription	Pancreas	Pancrea
15	chr10:5900400-5916200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr10:5900600-5916200	Weak transcription	Stomach Smooth Muscle	stomach
17	chr10:5900800-5910600	Weak transcription	Brain Germinal Matrix	brain
18	chr10:5901000-5904200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr10:5901000-5916600	Weak transcription	Gastric	stomach
20	chr10:5901200-5903200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr10:5901200-5903200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr10:5901200-5904200	Weak transcription	Brain Angular Gyrus	brain
23	chr10:5901200-5918200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr10:5901400-5905000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr10:5901400-5915200	Weak transcription	Brain Hippocampus Middle	brain
26	chr10:5901600-5904200	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr10:5901600-5912600	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr10:5901600-5915600	Weak transcription	Brain Anterior Caudate	brain
29	chr10:5901800-5904200	Weak transcription	Fetal Intestine Small	intestine
30	chr10:5901800-5910800	Weak transcription	Fetal Brain Female	brain
31	chr10:5902000-5902600	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr10:5902000-5902600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr10:5902000-5902600	Enhancers	Fetal Muscle Leg	muscle
34	chr10:5902000-5904000	Enhancers	GM12878-XiMat	blood
35	chr10:5902000-5904800	Enhancers	Placenta	Placenta
36	chr10:5902200-5902600	Weak transcription	Brain Substantia Nigra	brain
37	chr10:5902200-5903000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr10:5902200-5904600	Enhancers	NHDF-Ad	bronchial
39	chr10:5902200-5905000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr10:5902200-5912600	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr10:5902400-5902800	Enhancers	NHLF	lung
42	chr10:5902400-5904400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr10:5902400-5905000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
44	chr10:5902400-5908600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr10:5902400-5918200	Weak transcription	Primary T cells from cord blood	blood

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