Variant report

Variant	rs9332658
Chromosome Location	chr1:169489946-169489947
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:169484527..169487185-chr1:169488820..169490773,2	K562	blood:
2	chr1:169449894..169459462-chr1:169475885..169501963,75	MCF-7	breast:
3	chr1:169464611..169466208-chr1:169487405..169490324,2	K562	blood:
4	chr1:169481912..169483495-chr1:169489878..169491578,2	MCF-7	breast:
5	chr1:169451766..169456144-chr1:169486998..169490272,6	MCF-7	breast:
6	chr1:169486047..169488375-chr1:169489755..169492077,3	MCF-7	breast:
7	chr1:169488300..169490005-chr1:169506177..169508361,2	MCF-7	breast:

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

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1028180	1.00[CEU][hapmap]
rs12022009	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12040141	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12042044	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12733001	1.00[CEU][hapmap]
rs12733037	1.00[CEU][hapmap]
rs12752953	1.00[CEU][hapmap]
rs13306334	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1533518	1.00[CEU][hapmap]
rs1533519	1.00[CEU][hapmap]
rs16862097	1.00[CEU][hapmap]
rs16862176	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs16862180	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs16862217	1.00[CEU][hapmap]
rs1883167	1.00[CEU][hapmap]
rs2037249	1.00[CEU][hapmap]
rs2271762	1.00[CEU][hapmap]
rs2301517	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3213586	1.00[CEU][hapmap]
rs3213587	1.00[CEU][hapmap]
rs3862937	1.00[CEU][hapmap]
rs4140538	1.00[CEU][hapmap]
rs4140539	1.00[CEU][hapmap]
rs56273826	0.91[AFR][1000 genomes]
rs6008	0.95[EUR][1000 genomes]
rs6020	0.81[CHD][hapmap];0.81[GIH][hapmap]
rs66737090	0.95[EUR][1000 genomes]
rs7551623	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9332593	0.87[LWK][hapmap];1.00[YRI][hapmap]
rs9332623	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9332624	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.84[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9332628	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9332634	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs9332647	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9332678	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169481800-169493000	Strong transcription	Liver	Liver
2	chr1:169482600-169490800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr1:169483200-169495400	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr1:169483200-169496800	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr1:169483800-169496800	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr1:169484200-169494400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr1:169484800-169490400	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr1:169484800-169490400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr1:169484800-169501000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr1:169485400-169510600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr1:169486600-169494400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr1:169486800-169490400	Strong transcription	HepG2	liver
13	chr1:169487000-169490600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr1:169487400-169501000	Weak transcription	Right Ventricle	heart
15	chr1:169487800-169490200	Weak transcription	Stomach Mucosa	stomach
16	chr1:169488000-169492800	Weak transcription	Hela-S3	cervix
17	chr1:169488000-169493000	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr1:169488400-169490200	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr1:169489000-169490200	Weak transcription	Small Intestine	intestine
20	chr1:169489600-169490400	Enhancers	Duodenum Mucosa	Duodenum
21	chr1:169489800-169492000	Strong transcription	Placenta	Placenta
22	chr1:169489800-169494600	Weak transcription	Primary T helper cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links