Variant report

Variant	rs1851378
Chromosome Location	chr3:160513520-160513521
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:160513259..160516252-chr3:160518883..160520924,2	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10513553	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs12486979	0.81[EUR][1000 genomes]
rs12487861	0.89[ASW][hapmap];0.83[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.82[YRI][hapmap];0.89[ASN][1000 genomes]
rs12494732	0.85[JPT][hapmap]
rs13068380	0.91[EUR][1000 genomes]
rs13080397	0.85[JPT][hapmap]
rs1378654	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1378655	0.80[EUR][1000 genomes]
rs1378656	0.80[EUR][1000 genomes]
rs1378657	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1378658	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs1403048	0.80[EUR][1000 genomes]
rs1455869	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1598495	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1829716	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1839017	0.85[JPT][hapmap]
rs1902282	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1915929	0.92[AFR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2049214	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2049215	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2886905	0.81[EUR][1000 genomes]
rs4256178	0.85[JPT][hapmap]
rs59542611	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6775743	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6781371	0.81[EUR][1000 genomes]
rs6794047	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6805905	0.81[EUR][1000 genomes]
rs718757	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs722871	0.89[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs7618832	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7630250	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7634342	0.81[EUR][1000 genomes]
rs7640348	0.82[EUR][1000 genomes]
rs7642371	0.81[EUR][1000 genomes]
rs7643513	0.80[EUR][1000 genomes]
rs7648363	0.85[JPT][hapmap]
rs779058	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs897494	0.80[EUR][1000 genomes]
rs972909	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9814394	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9815499	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9833075	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9866566	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9868489	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs9869116	0.85[JPT][hapmap]
rs9883862	0.80[EUR][1000 genomes]

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	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv1009249	chr3:160496237-160627378	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv536780	chr3:160496237-160627378	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160498400-160522600	Weak transcription	Right Ventricle	heart
2	chr3:160503600-160514600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr3:160508600-160513600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr3:160509000-160514000	Weak transcription	Adipose Nuclei	Adipose
5	chr3:160509000-160522600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr3:160509600-160519000	Weak transcription	Stomach Smooth Muscle	stomach
7	chr3:160510400-160514200	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr3:160510600-160513600	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr3:160510800-160514000	Weak transcription	Right Atrium	heart
10	chr3:160511200-160515000	Enhancers	Fetal Heart	heart
11	chr3:160511400-160518400	Weak transcription	Primary T cells from cord blood	blood
12	chr3:160511800-160519800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:160512200-160515600	Enhancers	Stomach Mucosa	stomach
14	chr3:160512600-160514000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr3:160512600-160514200	Enhancers	Left Ventricle	heart
16	chr3:160512600-160514200	Enhancers	Psoas Muscle	Psoas
17	chr3:160512600-160514400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr3:160512600-160515600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr3:160512800-160514400	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr3:160512800-160519400	Weak transcription	Colon Smooth Muscle	Colon
21	chr3:160513200-160513600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr3:160513200-160514200	Enhancers	HUES48 Cell Line	embryonic stem cell
23	chr3:160513200-160515200	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr3:160513400-160513800	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr3:160513400-160519000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr3:160513400-160522600	Weak transcription	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links