Variant report

Variant	rs2270739
Chromosome Location	chr12:57429975-57429976
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	chr12:57429267..57431229-chr12:57431825..57433924,2	MCF-7	breast:
2	chr12:57425392..57428164-chr12:57428650..57431698,4	K562	blood:

Variant related genes	Relation type
ENSG00000166866	Chromatin interaction

Extended variants
information (count: 121 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:117)

rs_ID	r²[population]
rs10400412	0.94[ASN][1000 genomes]
rs10400555	0.94[ASN][1000 genomes]
rs1044939	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10506350	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10506351	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1072670	0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11832487	0.88[ASN][1000 genomes]
rs11834851	0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11834856	0.90[ASN][1000 genomes]
rs11836517	0.90[ASN][1000 genomes]
rs12099695	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12810024	0.80[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs12810837	0.89[ASN][1000 genomes]
rs12812499	0.89[ASN][1000 genomes]
rs12815538	0.90[ASN][1000 genomes]
rs12818342	0.90[ASN][1000 genomes]
rs12824682	0.90[ASN][1000 genomes]
rs12827039	0.90[ASN][1000 genomes]
rs12827286	0.86[ASN][1000 genomes]
rs1552245	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs17119301	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs17119327	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17119330	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17119344	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs17119352	0.99[ASN][1000 genomes]
rs17119386	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17119388	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17119390	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs17119407	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17119416	0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs17119418	0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1843311	0.90[ASN][1000 genomes]
rs1843312	0.90[ASN][1000 genomes]
rs1843313	0.90[ASN][1000 genomes]
rs2035545	0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs2167306	0.90[ASN][1000 genomes]
rs2233267	0.81[ASN][1000 genomes]
rs2270736	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2270737	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2279373	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2279743	0.93[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2291855	1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs2371717	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs28589663	0.90[ASN][1000 genomes]
rs2888139	0.89[ASN][1000 genomes]
rs3024974	0.80[CHB][hapmap]
rs34186462	0.90[ASN][1000 genomes]
rs34253098	0.90[ASN][1000 genomes]
rs34359134	0.90[ASN][1000 genomes]
rs34762603	0.90[ASN][1000 genomes]
rs34969650	0.90[ASN][1000 genomes]
rs35034299	0.90[ASN][1000 genomes]
rs35243318	0.90[ASN][1000 genomes]
rs35493121	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs35937600	0.82[ASN][1000 genomes]
rs3759134	0.80[ASN][1000 genomes]
rs3759135	0.81[ASN][1000 genomes]
rs3782329	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3782330	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3803018	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3894415	0.91[ASN][1000 genomes]
rs4016338	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4039	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4143085	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs56128678	0.99[ASN][1000 genomes]
rs56270558	0.99[ASN][1000 genomes]
rs56354404	0.99[ASN][1000 genomes]
rs57056392	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57129030	0.90[ASN][1000 genomes]
rs57351760	0.89[ASN][1000 genomes]
rs57558853	0.94[ASN][1000 genomes]
rs58298943	0.91[ASN][1000 genomes]
rs58389529	0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs60258120	0.89[ASN][1000 genomes]
rs60273384	0.93[ASN][1000 genomes]
rs60380217	0.90[ASN][1000 genomes]
rs61504157	1.00[ASN][1000 genomes]
rs66741626	0.82[ASN][1000 genomes]
rs67476535	0.93[ASN][1000 genomes]
rs67771054	0.90[ASN][1000 genomes]
rs67844278	0.91[ASN][1000 genomes]
rs68126184	0.91[ASN][1000 genomes]
rs697222	0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs7135297	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7136770	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs71461303	0.89[ASN][1000 genomes]
rs72482268	0.91[ASN][1000 genomes]
rs7298475	0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs73114426	0.94[ASN][1000 genomes]
rs73114428	0.94[ASN][1000 genomes]
rs73114434	0.94[ASN][1000 genomes]
rs73114436	0.94[ASN][1000 genomes]
rs73114437	0.96[ASN][1000 genomes]
rs73114446	0.99[ASN][1000 genomes]
rs73114452	0.99[ASN][1000 genomes]
rs73114457	0.99[ASN][1000 genomes]
rs73114459	0.99[ASN][1000 genomes]
rs73114467	0.99[ASN][1000 genomes]
rs73114468	0.99[ASN][1000 genomes]
rs73114472	0.96[ASN][1000 genomes]
rs73116494	0.90[ASN][1000 genomes]
rs73116501	0.90[ASN][1000 genomes]
rs73118413	0.88[ASN][1000 genomes]
rs73118416	0.81[ASN][1000 genomes]
rs73118418	0.81[ASN][1000 genomes]
rs73131120	0.91[ASN][1000 genomes]
rs733629	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs746049	0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7487948	0.90[ASN][1000 genomes]
rs754398	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs755221	0.99[ASN][1000 genomes]
rs7956166	0.90[ASN][1000 genomes]
rs7961920	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7962771	0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7969312	0.90[ASN][1000 genomes]
rs7972615	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs901068	0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[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	nsv1040850	chr12:57055011-57679209	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	nsv428590	chr12:57329214-57527358	Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
3	nsv832428	chr12:57340609-57535694	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
4	nsv899110	chr12:57422934-57472502	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57416800-57439400	Strong transcription	Fetal Intestine Small	intestine
2	chr12:57417200-57441200	Weak transcription	Small Intestine	intestine
3	chr12:57419200-57439400	Strong transcription	Duodenum Mucosa	Duodenum
4	chr12:57419800-57439600	Strong transcription	Fetal Intestine Large	intestine
5	chr12:57420000-57440000	Strong transcription	Rectal Mucosa Donor 29	rectum
6	chr12:57420400-57471800	Weak transcription	Gastric	stomach
7	chr12:57421800-57441600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr12:57424200-57431400	Weak transcription	Fetal Stomach	stomach
9	chr12:57424200-57431600	Weak transcription	Colonic Mucosa	Colon
10	chr12:57425600-57432000	Weak transcription	K562	blood
11	chr12:57426000-57433000	Weak transcription	Fetal Thymus	thymus
12	chr12:57426000-57433200	Weak transcription	Thymus	Thymus
13	chr12:57426400-57433200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr12:57426600-57432200	Weak transcription	Placenta	Placenta
15	chr12:57427000-57433200	Weak transcription	Primary T cells from cord blood	blood
16	chr12:57427400-57435400	Strong transcription	Sigmoid Colon	Sigmoid Colon
17	chr12:57429000-57438000	Strong transcription	Rectal Mucosa Donor 31	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links