Variant report

Variant	rs2408083
Chromosome Location	chr12:45231024-45231025
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:45228200..45231167-chr12:45235682..45238420,2	K562	blood:
2	chr12:45229297..45232222-chr12:45268941..45271789,2	K562	blood:

Variant related genes	Relation type
ENSG00000184613	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10161447	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10506258	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10785535	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10785536	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10785537	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10785538	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10785540	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11182754	0.82[EUR][1000 genomes]
rs11504491	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11524561	0.82[AMR][1000 genomes]
rs11833874	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12227370	0.95[EUR][1000 genomes]
rs12316579	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12818329	0.89[EUR][1000 genomes]
rs1376126	0.92[CEU][hapmap];0.81[AMR][1000 genomes]
rs1395397	0.92[CEU][hapmap];0.88[CHB][hapmap];0.93[JPT][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1506679	0.85[CEU][hapmap]
rs1605296	0.80[CEU][hapmap];0.93[CHB][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1605297	0.92[CEU][hapmap];0.94[CHB][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1605298	0.92[CEU][hapmap];0.94[CHB][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17095127	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1857927	0.85[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2055675	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2055676	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2055677	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2258058	0.84[AMR][1000 genomes]
rs2408084	0.92[CEU][hapmap];0.85[GIH][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2408085	1.00[CEU][hapmap];0.85[GIH][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2465109	0.85[AMR][1000 genomes]
rs2658948	0.83[CEU][hapmap]
rs2658954	0.81[EUR][1000 genomes]
rs2658957	0.92[CEU][hapmap];0.94[CHB][hapmap];0.85[AMR][1000 genomes]
rs2658959	0.82[AMR][1000 genomes]
rs2658965	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2658966	0.90[CEU][hapmap];0.92[CHB][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2710453	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2710455	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2710457	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2710459	0.92[CEU][hapmap];0.94[CHB][hapmap];0.83[CHD][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2710460	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2710461	0.85[AMR][1000 genomes]
rs2710462	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4238095	0.92[CEU][hapmap];0.94[CHB][hapmap];0.83[CHD][hapmap];0.94[GIH][hapmap];0.95[MEX][hapmap];0.85[AMR][1000 genomes]
rs4300447	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4415832	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4499065	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4768075	0.92[CEU][hapmap];0.94[CHB][hapmap];0.83[CHD][hapmap];0.97[GIH][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes]
rs4768577	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4768578	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55741117	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56892258	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57190502	0.95[EUR][1000 genomes]
rs74079970	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7957052	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7957160	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7960817	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs7971834	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7973268	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7975618	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7976293	0.86[CHB][hapmap];0.93[JPT][hapmap]
rs884259	0.92[CEU][hapmap];0.94[CHB][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs884260	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs978696	0.82[CHB][hapmap];0.93[JPT][hapmap];0.82[MEX][hapmap]

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	esv3378050	chr12:44963059-45264289	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv832394	chr12:45077573-45269305	Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
3	nsv1036926	chr12:45131884-45273648	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
4	nsv541484	chr12:45131884-45273648	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:45213600-45237800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:45220600-45242000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
3	chr12:45221800-45242000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr12:45225200-45231400	Enhancers	Fetal Intestine Small	intestine
5	chr12:45228000-45231200	Enhancers	Fetal Intestine Large	intestine
6	chr12:45228000-45231400	Enhancers	Duodenum Mucosa	Duodenum
7	chr12:45228800-45231800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr12:45228800-45232000	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr12:45228800-45234200	Enhancers	Primary T cells from cord blood	blood
10	chr12:45229000-45231200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chr12:45229000-45231600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr12:45229600-45231200	Weak transcription	Brain Angular Gyrus	brain
13	chr12:45229600-45233800	Weak transcription	Esophagus	oesophagus
14	chr12:45230000-45242200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr12:45230200-45231200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:45230200-45231400	Enhancers	Primary T cells fromperipheralblood	blood
17	chr12:45230200-45232600	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr12:45230400-45233200	Weak transcription	Fetal Brain Female	brain
19	chr12:45230400-45236600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr12:45230600-45232600	Weak transcription	Fetal Brain Male	brain
21	chr12:45230600-45234000	Enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr12:45230800-45237400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr12:45231000-45231200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr12:45231000-45231200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--

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