Variant report

Variant	rs560900
Chromosome Location	chr1:193282883-193282884
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:193278831..193281836-chr1:193282854..193285758,3	K562	blood:
2	chr1:193277193..193280125-chr1:193280849..193282913,2	MCF-7	breast:
3	chr1:193282788..193284410-chr1:193285163..193288085,2	K562	blood:

Extended variants
information (count: 140 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:136)

rs_ID	r²[population]
rs10399607	0.81[EUR][1000 genomes]
rs10399929	0.80[EUR][1000 genomes]
rs10494674	0.95[CEU][hapmap];0.82[CHB][hapmap]
rs10732293	0.91[CHB][hapmap]
rs10733078	0.91[CHB][hapmap];0.82[GIH][hapmap]
rs10737621	0.94[CHB][hapmap]
rs10737622	0.86[CEU][hapmap];0.91[CHB][hapmap]
rs10737623	0.85[EUR][1000 genomes]
rs10754044	0.95[CEU][hapmap];0.91[CHB][hapmap]
rs10754047	0.90[CEU][hapmap];0.91[CHB][hapmap]
rs10754048	0.95[CEU][hapmap];0.91[CHB][hapmap]
rs10754049	0.95[CEU][hapmap];0.91[CHB][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs10754052	0.95[CEU][hapmap];0.90[CHB][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs10754053	0.81[EUR][1000 genomes]
rs10754054	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10754055	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10801177	0.91[CHB][hapmap];0.82[GIH][hapmap]
rs10801178	0.91[CHB][hapmap]
rs10801179	0.95[CEU][hapmap];0.91[CHB][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs10801183	0.95[CEU][hapmap];0.91[CHB][hapmap]
rs10801184	0.91[CHB][hapmap];0.82[GIH][hapmap]
rs10801187	0.91[CHB][hapmap]
rs10801189	0.91[CHB][hapmap];0.82[GIH][hapmap]
rs10801194	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10921318	0.91[CHB][hapmap]
rs10921323	0.91[CHB][hapmap]
rs10921325	0.95[CEU][hapmap];0.97[GIH][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.81[EUR][1000 genomes]
rs10921326	0.91[CHB][hapmap];0.82[GIH][hapmap]
rs10921330	0.91[CHB][hapmap]
rs10921336	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10921343	0.86[EUR][1000 genomes]
rs11577299	0.91[CHB][hapmap];0.82[GIH][hapmap]
rs12025186	0.81[EUR][1000 genomes]
rs12025393	0.82[EUR][1000 genomes]
rs12032958	0.82[EUR][1000 genomes]
rs12034095	0.89[EUR][1000 genomes]
rs12037055	0.89[EUR][1000 genomes]
rs12040365	0.89[EUR][1000 genomes]
rs12040832	0.83[EUR][1000 genomes]
rs12041558	0.83[EUR][1000 genomes]
rs12041893	0.89[EUR][1000 genomes]
rs12047390	0.90[CEU][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs12048579	0.83[EUR][1000 genomes]
rs12090626	0.91[CHB][hapmap];0.89[GIH][hapmap]
rs12126529	0.83[ASW][hapmap];0.95[CEU][hapmap];0.91[CHB][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs12145057	0.91[CHB][hapmap]
rs1221502	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12410213	0.90[CHB][hapmap]
rs1325197	0.90[CEU][hapmap];0.90[CHB][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.81[EUR][1000 genomes]
rs1339961	0.87[EUR][1000 genomes]
rs1361405	0.90[CEU][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs1408830	0.91[CHB][hapmap];0.82[GIH][hapmap]
rs1416977	0.97[ASN][1000 genomes]
rs1536097	0.81[EUR][1000 genomes]
rs1536098	0.91[CHB][hapmap]
rs1536099	0.91[CHB][hapmap]
rs1616234	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1632444	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16835282	0.93[EUR][1000 genomes]
rs16835304	0.89[EUR][1000 genomes]
rs16835319	0.83[EUR][1000 genomes]
rs16835320	0.83[EUR][1000 genomes]
rs1749424	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1749429	0.86[EUR][1000 genomes]
rs1749430	0.92[EUR][1000 genomes]
rs1749431	0.92[EUR][1000 genomes]
rs1749432	0.93[EUR][1000 genomes]
rs1769999	0.93[EUR][1000 genomes]
rs1972344	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1972345	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2078083	0.86[EUR][1000 genomes]
rs2182106	0.95[CEU][hapmap];0.91[CHB][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs2186016	0.91[CHB][hapmap];0.82[GIH][hapmap]
rs2254646	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2275506	0.82[EUR][1000 genomes]
rs2370029	0.95[CEU][hapmap];0.91[CHB][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs2370264	0.96[ASN][1000 genomes]
rs2477549	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2486842	0.90[EUR][1000 genomes]
rs3738244	0.91[CHB][hapmap]
rs3806351	0.91[CHB][hapmap];0.82[GIH][hapmap]
rs4379660	0.95[CEU][hapmap];0.91[CHB][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs4450000	0.91[CHB][hapmap]
rs4466634	0.91[CHB][hapmap]
rs4657744	0.91[CHB][hapmap]
rs4657847	0.91[CHB][hapmap];0.82[GIH][hapmap]
rs4657848	0.95[CEU][hapmap];0.91[CHB][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs4657854	0.89[EUR][1000 genomes]
rs4657855	0.89[EUR][1000 genomes]
rs4657858	0.81[EUR][1000 genomes]
rs475163	0.89[EUR][1000 genomes]
rs497362	0.91[EUR][1000 genomes]
rs503265	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs515964	0.93[EUR][1000 genomes]
rs523402	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs524701	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs543788	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs569656	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs571029	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs578639	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59264807	0.93[EUR][1000 genomes]
rs6428152	0.86[CEU][hapmap];0.91[CHB][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap]
rs6428153	0.81[EUR][1000 genomes]
rs6428154	0.95[CEU][hapmap];0.90[CHB][hapmap];0.81[EUR][1000 genomes]
rs6428156	0.91[CHB][hapmap];0.82[GIH][hapmap]
rs6428157	0.91[CHB][hapmap];0.82[GIH][hapmap]
rs6428159	0.95[CEU][hapmap];0.91[CHB][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs6428160	0.86[EUR][1000 genomes]
rs6428163	0.89[EUR][1000 genomes]
rs6428166	0.89[EUR][1000 genomes]
rs6665666	0.95[CEU][hapmap];0.91[CHB][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs6671237	0.86[CEU][hapmap];0.91[CHB][hapmap];0.89[GIH][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap]
rs6671476	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6673271	0.95[CEU][hapmap];0.91[CHB][hapmap];0.94[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs6675833	0.95[CEU][hapmap];0.91[CHB][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.80[EUR][1000 genomes]
rs6676878	0.95[CEU][hapmap];0.91[CHB][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs6680224	0.95[CEU][hapmap];0.86[CHB][hapmap];0.81[EUR][1000 genomes]
rs6693734	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs6697079	0.86[CHB][hapmap];0.81[GIH][hapmap]
rs6697195	0.81[EUR][1000 genomes]
rs693519	0.91[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7514072	0.86[CHB][hapmap]
rs7515024	0.91[CHB][hapmap];0.87[GIH][hapmap]
rs7518792	0.86[CEU][hapmap];0.91[CHB][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap]
rs7519242	0.83[ASW][hapmap];0.95[CEU][hapmap];0.91[CHB][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs7528595	0.93[EUR][1000 genomes]
rs7545223	0.81[EUR][1000 genomes]
rs7550521	0.89[EUR][1000 genomes]
rs817136	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs817138	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs817140	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs817142	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs817143	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs843844	0.91[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs942680	0.87[EUR][1000 genomes]
rs9887974	0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832148	chr1:193143945-193292897	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv872831	chr1:193152317-193322087	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv1001174	chr1:193186758-193363372	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv997891	chr1:193271839-193566441	Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:193276600-193283400	Enhancers	Fetal Intestine Small	intestine
2	chr1:193277000-193283400	Enhancers	Fetal Intestine Large	intestine
3	chr1:193281000-193284400	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr1:193282200-193283000	Enhancers	Small Intestine	intestine
5	chr1:193282200-193283200	Enhancers	Rectal Mucosa Donor 31	rectum
6	chr1:193282600-193283000	Enhancers	HepG2	liver
7	chr1:193282600-193283400	Active TSS	Rectal Mucosa Donor 29	rectum
8	chr1:193282800-193283200	Flanking Active TSS	Duodenum Mucosa	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links