Variant report

Variant	rs981959
Chromosome Location	chr4:55526962-55526963
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:55526044..55527656-chr4:55529218..55531772,2	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10488849	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11727273	0.94[EUR][1000 genomes]
rs11940731	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12499367	0.90[EUR][1000 genomes]
rs12503461	0.83[MEX][hapmap]
rs12504135	0.90[EUR][1000 genomes]
rs2159935	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2192158	0.90[EUR][1000 genomes]
rs2192159	0.90[EUR][1000 genomes]
rs2237029	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.96[ASN][1000 genomes]
rs2237030	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2237037	1.00[CEU][hapmap]
rs2237038	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2855778	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3819386	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3819391	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3819393	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6554193	0.90[EUR][1000 genomes]
rs6554194	0.90[EUR][1000 genomes]
rs6554198	0.85[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.93[TSI][hapmap]
rs6554199	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap]
rs6554200	0.91[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6815651	0.84[EUR][1000 genomes]
rs6825293	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7679314	0.81[EUR][1000 genomes]
rs7695300	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs999020	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs999021	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008793	chr4:55060925-55535807	Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv537098	chr4:55060925-55535807	Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv999400	chr4:55143598-55776995	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv997430	chr4:55253397-55529288	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	esv3367952	chr4:55437113-55724644	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv1010702	chr4:55440944-55528450	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv526344	chr4:55522488-56231119	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:55523000-55528600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr4:55524800-55527200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr4:55525200-55527400	Flanking Active TSS	Primary hematopoietic stem cells	blood
4	chr4:55525800-55527000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr4:55525800-55528600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr4:55525800-55528600	Enhancers	NHLF	lung
7	chr4:55525800-55529200	Weak transcription	Aorta	Aorta
8	chr4:55525800-55537200	Weak transcription	Right Atrium	heart
9	chr4:55526000-55527000	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr4:55526000-55527800	Enhancers	Psoas Muscle	Psoas
11	chr4:55526000-55528600	Enhancers	NH-A	brain
12	chr4:55526200-55527200	Bivalent Enhancer	Fetal Brain Male	brain
13	chr4:55526200-55527600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr4:55526200-55527800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr4:55526400-55527000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
16	chr4:55526400-55527400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr4:55526400-55527600	Enhancers	NHEK	skin
18	chr4:55526400-55527800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr4:55526400-55528200	Weak transcription	Fetal Muscle Trunk	muscle
20	chr4:55526400-55528600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr4:55526400-55528600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr4:55526600-55527000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr4:55526600-55527000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr4:55526600-55527200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr4:55526600-55527200	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr4:55526600-55527200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr4:55526600-55527600	Weak transcription	Ovary	ovary
28	chr4:55526600-55527800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
29	chr4:55526600-55528600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr4:55526600-55531600	Weak transcription	Gastric	stomach
31	chr4:55526800-55527200	Enhancers	NHDF-Ad	bronchial
32	chr4:55526800-55528400	Enhancers	HMEC	breast
33	chr4:55526800-55528600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links