Variant report

Variant	rs12425900
Chromosome Location	chr12:25257990-25257991
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10505959	0.89[JPT][hapmap]
rs10505960	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10771174	1.00[JPT][hapmap]
rs10842466	0.84[ASN][1000 genomes]
rs10842468	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs10842473	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10842475	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10842492	0.83[ASN][1000 genomes]
rs11047823	0.86[ASN][1000 genomes]
rs11047824	0.84[ASN][1000 genomes]
rs11047846	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11047849	0.81[ASN][1000 genomes]
rs11047854	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11047855	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11047856	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11047858	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs11047865	0.82[ASN][1000 genomes]
rs11513449	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11609915	0.80[ASN][1000 genomes]
rs11832421	0.84[ASN][1000 genomes]
rs11832456	0.84[ASN][1000 genomes]
rs12227966	0.84[JPT][hapmap]
rs12424685	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12581134	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12818169	0.87[ASN][1000 genomes]
rs12828225	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12828609	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12830058	0.83[ASN][1000 genomes]
rs12830336	0.83[ASN][1000 genomes]
rs1497253	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs1908946	0.82[ASN][1000 genomes]
rs2291365	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2352782	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2352784	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4559767	0.87[ASN][1000 genomes]
rs4963848	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4963850	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61020746	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6487456	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7297103	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7976254	0.89[JPT][hapmap]

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	nsv469169	chr12:24692383-25357680	Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv557775	chr12:24692383-25357680	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv932477	chr12:24705151-25346677	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv1067577	chr12:24791283-25346677	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv529514	chr12:24791283-25346677	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv1041218	chr12:24972019-25304356	Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:25209400-25264400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr12:25210000-25262800	Weak transcription	Duodenum Mucosa	Duodenum
3	chr12:25215000-25265000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr12:25230000-25264600	Strong transcription	Fetal Thymus	thymus
5	chr12:25232200-25263600	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr12:25238600-25263000	Weak transcription	Left Ventricle	heart
7	chr12:25238600-25265200	Weak transcription	Lung	lung
8	chr12:25242800-25262200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr12:25243000-25259200	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr12:25246400-25264000	Weak transcription	Ovary	ovary
11	chr12:25247400-25258400	Strong transcription	Primary T cells from cord blood	blood
12	chr12:25247800-25258000	Strong transcription	Primary B cells from cord blood	blood
13	chr12:25248400-25262800	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr12:25248600-25258600	Strong transcription	Primary hematopoietic stem cells	blood
15	chr12:25248600-25264400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr12:25248800-25258000	Strong transcription	Dnd41	blood
17	chr12:25248800-25258400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr12:25248800-25259200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr12:25249200-25261800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr12:25251800-25274600	Weak transcription	Pancreas	Pancrea
21	chr12:25252200-25264000	Weak transcription	Spleen	Spleen
22	chr12:25252400-25260400	Weak transcription	Adipose Nuclei	Adipose
23	chr12:25253200-25262800	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr12:25254000-25260200	Strong transcription	Primary B cells from peripheral blood	blood
25	chr12:25254200-25259800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr12:25254200-25260400	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr12:25254200-25263600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr12:25254200-25263800	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr12:25254200-25263800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr12:25254400-25260600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr12:25255600-25260400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr12:25255800-25260200	Weak transcription	Thymus	Thymus
33	chr12:25255800-25261400	Weak transcription	Small Intestine	intestine
34	chr12:25255800-25262400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr12:25256000-25260400	Weak transcription	Liver	Liver
36	chr12:25256000-25265200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr12:25256800-25262600	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr12:25257000-25264800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr12:25257400-25258600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr12:25257400-25264800	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr12:25257600-25259800	Weak transcription	GM12878-XiMat	blood
42	chr12:25257800-25260400	Weak transcription	Primary T helper cells PMA-I stimulated	--

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