Variant report

Variant	rs1534472
Chromosome Location	chr2:177677940-177677941
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:177581802..177583651-chr2:177676753..177679006,2	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10181816	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10184702	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10197209	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10497573	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12469347	1.00[CHB][hapmap]
rs12693105	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1437725	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1513886	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1533303	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1545138	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.84[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16864475	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16864479	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4021386	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4893917	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6740977	0.86[ASN][1000 genomes]
rs72936904	0.82[ASN][1000 genomes]
rs7588841	1.00[CHB][hapmap]
rs7601162	0.86[ASN][1000 genomes]
rs840698	1.00[CHB][hapmap]
rs840699	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv527737	chr2:177538266-177692572	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv583686	chr2:177538266-177692572	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1006500	chr2:177548521-177707097	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:177676400-177679000	Enhancers	Brain Germinal Matrix	brain
2	chr2:177676600-177678200	Enhancers	Fetal Brain Male	brain
3	chr2:177676600-177678800	Enhancers	Fetal Brain Female	brain
4	chr2:177676800-177678600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
5	chr2:177676800-177679600	Enhancers	Fetal Lung	lung
6	chr2:177677000-177679000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr2:177677200-177678200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr2:177677200-177678200	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr2:177677200-177679200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr2:177677200-177679600	Enhancers	Ovary	ovary
11	chr2:177677400-177678000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr2:177677400-177678000	Weak transcription	Brain Anterior Caudate	brain
13	chr2:177677400-177678400	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr2:177677400-177678600	Enhancers	Brain Hippocampus Middle	brain
15	chr2:177677400-177681600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr2:177677600-177678000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr2:177677600-177678400	Weak transcription	Adipose Nuclei	Adipose
18	chr2:177677600-177678600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr2:177677800-177678200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links