Variant report

Variant	rs2301517
Chromosome Location	chr1:169494403-169494404
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:169449894..169459462-chr1:169475885..169501963,75	MCF-7	breast:
2	chr1:169480439..169483097-chr1:169493507..169495167,2	MCF-7	breast:
3	chr1:169352595..169354140-chr1:169494261..169496429,2	MCF-7	breast:
4	chr1:169475721..169488506-chr1:169493331..169501885,21	MCF-7	breast:
5	chr1:169483273..169484944-chr1:169493711..169496257,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000213062	Chromatin interaction
ENSG00000117479	Chromatin interaction
ENSG00000198734	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12022009	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12040141	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12042044	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13306334	0.94[CHB][hapmap];0.90[JPT][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16862176	0.82[EUR][1000 genomes]
rs16862180	0.82[EUR][1000 genomes]
rs6008	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs66737090	0.95[EUR][1000 genomes]
rs7551623	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9332623	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9332624	0.89[CHB][hapmap];0.90[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9332628	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9332647	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9332658	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9332678	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[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	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer 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	56 gene(s)	inside rSNPs	diseases
2	nsv872533	chr1:169490401-169508576	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169483200-169495400	Strong transcription	Primary neutrophils fromperipheralblood	blood
2	chr1:169483200-169496800	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr1:169483800-169496800	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr1:169484800-169501000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr1:169485400-169510600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr1:169487400-169501000	Weak transcription	Right Ventricle	heart
7	chr1:169489800-169494600	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr1:169490600-169496200	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr1:169490800-169494600	Weak transcription	Duodenum Mucosa	Duodenum
10	chr1:169490800-169496200	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr1:169490800-169496800	Weak transcription	Pancreas	Pancrea
12	chr1:169490800-169496800	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr1:169491200-169497000	Weak transcription	Small Intestine	intestine
14	chr1:169491600-169500800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr1:169492000-169499800	Weak transcription	Left Ventricle	heart
16	chr1:169492800-169495400	Enhancers	Hela-S3	cervix
17	chr1:169493000-169496000	Genic enhancers	Liver	Liver
18	chr1:169493600-169494800	Weak transcription	Stomach Mucosa	stomach
19	chr1:169494000-169496200	Weak transcription	Placenta	Placenta
20	chr1:169494000-169496800	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr1:169494000-169502800	Strong transcription	HepG2	liver
22	chr1:169494400-169495200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr1:169494400-169495600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr1:169494400-169496400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr1:169494400-169498000	Enhancers	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links