Variant report

Variant	rs9423597
Chromosome Location	chr10:5336050-5336051
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:5333712..5336149-chr10:5487099..5489733,2	MCF-7	breast:
2	chr10:4869978..4871994-chr10:5334140..5336719,2	K562	blood:
3	chr10:5056816..5057785-chr10:5335747..5336705,2	MCF-7	breast:
4	chr10:5335891..5336750-chr10:5390020..5390722,2	MCF-7	breast:
5	chr10:5336048..5336657-chr10:5385291..5386158,2	MCF-7	breast:
6	chr10:5336010..5336717-chr10:5425689..5426611,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000173848	Chromatin interaction
ENSG00000151632	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs2895073	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs4881429	0.81[EUR][1000 genomes]
rs7076488	0.83[CEU][hapmap];0.80[EUR][1000 genomes]
rs7094891	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs9423403	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9423593	0.95[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9423594	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894792	chr10:4832920-5498724	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv534685	chr10:4914018-5853324	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
3	nsv1039386	chr10:5008383-5348491	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv1036291	chr10:5076258-5456234	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv932104	chr10:5203626-5641023	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
6	nsv549886	chr10:5205437-5632060	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
7	nsv1054865	chr10:5225305-5638119	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
8	nsv466715	chr10:5285597-5348491	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv466717	chr10:5285597-5348491	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv549888	chr10:5285597-5348491	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv894795	chr10:5286600-5348491	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv894796	chr10:5300976-5348491	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:5326600-5337200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr10:5332800-5336600	Enhancers	Primary hematopoietic stem cells short term culture	blood
3	chr10:5333000-5336600	Enhancers	HMEC	breast
4	chr10:5333200-5336600	Enhancers	HUVEC	blood vessel
5	chr10:5333400-5336600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr10:5333600-5336400	Enhancers	Esophagus	oesophagus
7	chr10:5333600-5336400	Enhancers	Skeletal Muscle Male	skeletal muscle
8	chr10:5333600-5336600	Enhancers	Fetal Thymus	thymus
9	chr10:5333800-5336400	Enhancers	Adipose Nuclei	Adipose
10	chr10:5334200-5336600	Enhancers	Left Ventricle	heart
11	chr10:5334200-5336600	Enhancers	NHEK	skin
12	chr10:5334200-5338800	Weak transcription	HSMM	muscle
13	chr10:5334400-5336400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr10:5334400-5336400	Active TSS	Primary T killer memory cells from peripheral blood	blood
15	chr10:5334400-5336600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr10:5334400-5337400	Weak transcription	Psoas Muscle	Psoas
17	chr10:5334400-5338600	Weak transcription	HSMMtube	muscle
18	chr10:5334400-5338800	Weak transcription	Small Intestine	intestine
19	chr10:5334400-5340400	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr10:5334600-5336200	Active TSS	Primary T cells from cord blood	blood
21	chr10:5334600-5336200	Weak transcription	Spleen	Spleen
22	chr10:5334600-5336400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr10:5334600-5336600	Enhancers	Stomach Mucosa	stomach
24	chr10:5334600-5337400	Weak transcription	K562	blood
25	chr10:5334600-5338200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr10:5334600-5339400	Enhancers	Primary neutrophils fromperipheralblood	blood
27	chr10:5335000-5336600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
28	chr10:5335000-5338600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
29	chr10:5335200-5336800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
30	chr10:5335200-5339400	Weak transcription	Hela-S3	cervix
31	chr10:5335400-5336200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
32	chr10:5335400-5336800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
33	chr10:5335600-5336200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr10:5335600-5336400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr10:5335600-5336400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr10:5335600-5336400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr10:5335600-5336400	Enhancers	Primary hematopoietic stem cells	blood
38	chr10:5335600-5336400	Enhancers	Muscle Satellite Cultured Cells	--
39	chr10:5335600-5336400	Enhancers	Lung	lung
40	chr10:5335600-5336400	Enhancers	Sigmoid Colon	Sigmoid Colon
41	chr10:5335600-5336400	Enhancers	Thymus	Thymus
42	chr10:5335600-5336600	Enhancers	HUES6 Cell Line	embryonic stem cell
43	chr10:5335600-5336600	Enhancers	Primary B cells from cord blood	blood
44	chr10:5335600-5336600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
45	chr10:5335600-5336600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
46	chr10:5335600-5336600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
47	chr10:5335600-5336600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
48	chr10:5335600-5336600	Enhancers	Placenta	Placenta
49	chr10:5335600-5336600	Enhancers	Rectal Mucosa Donor 31	rectum
50	chr10:5335600-5336600	Flanking Active TSS	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links