Variant report

Variant	rs12477360
Chromosome Location	chr2:231161005-231161006
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 103 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10164566	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10177685	0.81[ASN][1000 genomes]
rs10200874	0.81[ASN][1000 genomes]
rs10498245	0.85[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs10498250	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs10933332	0.85[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs10933333	0.85[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs11890934	0.81[ASN][1000 genomes]
rs11896138	0.81[ASN][1000 genomes]
rs11900220	0.81[ASN][1000 genomes]
rs11900550	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs12472020	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13389060	0.84[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];0.83[EUR][1000 genomes]
rs13395371	0.81[ASN][1000 genomes]
rs13422994	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1346311	0.84[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];0.83[EUR][1000 genomes]
rs1579396	0.81[ASN][1000 genomes]
rs16826952	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16827171	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs16827179	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs1863674	0.91[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1863677	0.81[ASN][1000 genomes]
rs2081713	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2114588	0.86[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs2114590	0.85[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs2162481	0.85[CHB][hapmap];0.89[JPT][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2396741	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34839676	0.81[ASN][1000 genomes]
rs3769841	0.84[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3769842	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3769843	0.81[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3769844	0.84[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3769846	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3813464	0.81[ASN][1000 genomes]
rs3820975	0.84[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];0.88[EUR][1000 genomes]
rs3829782	0.89[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4343458	0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4972943	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4972945	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4972948	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs4972951	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs4973302	0.91[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.90[EUR][1000 genomes]
rs4973304	0.86[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs4973305	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4973306	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4973314	0.81[ASN][1000 genomes]
rs4973315	0.86[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs4973317	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs4973318	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs57003673	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57168851	0.81[ASN][1000 genomes]
rs57402789	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59020873	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59191607	0.81[ASN][1000 genomes]
rs59352509	0.81[ASN][1000 genomes]
rs59805999	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61575136	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62191186	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62191188	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62191189	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62191191	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62191192	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62191193	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62191196	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62191197	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62191199	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62191200	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62191201	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62191202	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62192161	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62193107	0.90[EUR][1000 genomes]
rs62193138	0.90[EUR][1000 genomes]
rs62193139	0.90[EUR][1000 genomes]
rs62193140	0.90[EUR][1000 genomes]
rs62193141	0.90[EUR][1000 genomes]
rs62193142	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62193143	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62193147	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6732442	0.81[ASN][1000 genomes]
rs6756713	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs67864003	0.81[ASN][1000 genomes]
rs72495165	0.91[ASN][1000 genomes]
rs72495166	0.81[ASN][1000 genomes]
rs72495167	0.81[ASN][1000 genomes]
rs73110326	0.81[ASN][1000 genomes]
rs73110329	0.81[ASN][1000 genomes]
rs73110331	0.81[ASN][1000 genomes]
rs73110337	0.81[ASN][1000 genomes]
rs73110339	0.81[ASN][1000 genomes]
rs73110345	0.81[ASN][1000 genomes]
rs73110346	0.81[ASN][1000 genomes]
rs73110350	0.81[ASN][1000 genomes]
rs73110356	0.81[ASN][1000 genomes]
rs7576496	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[EUR][1000 genomes]
rs7591582	0.91[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.90[EUR][1000 genomes]
rs9989792	0.85[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs9989808	0.85[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001562	chr2:230862717-231187043	Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv536156	chr2:230862717-231187043	Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv498047	chr2:230951712-231250489	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	esv18000	chr2:231072978-231467847	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	esv3417154	chr2:231159789-231258938	Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	esv3348338	chr2:231160124-231259498	Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:231090200-231170000	Weak transcription	Spleen	Spleen
2	chr2:231128200-231166000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr2:231147200-231165400	Strong transcription	Primary T cells fromperipheralblood	blood
4	chr2:231147800-231182400	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr2:231152800-231161200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
6	chr2:231153000-231161200	Strong transcription	Primary T helper cells PMA-I stimulated	--
7	chr2:231153000-231165400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr2:231153400-231165400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr2:231153800-231183400	Weak transcription	Duodenum Mucosa	Duodenum
10	chr2:231154000-231165400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr2:231154600-231164400	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr2:231158400-231165400	Strong transcription	Primary T cells from cord blood	blood
13	chr2:231158400-231165800	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr2:231159600-231165000	ZNF genes & repeats	GM12878-XiMat	blood
15	chr2:231160600-231161400	ZNF genes & repeats	Primary B cells from cord blood	blood
16	chr2:231160600-231162200	ZNF genes & repeats	Primary B cells from peripheral blood	blood
17	chr2:231160800-231161600	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
18	chr2:231160800-231161800	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
19	chr2:231161000-231161400	ZNF genes & repeats	Primary T killer memory cells from peripheral blood	blood
20	chr2:231161000-231161600	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
21	chr2:231161000-231161800	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood

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