Variant report

Variant	rs12438452
Chromosome Location	chr15:56417930-56417931
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10444835	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11071244	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11071248	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11071251	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11071256	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12437466	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12438262	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12438525	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12438606	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12438670	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12439033	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12439133	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12440495	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12440509	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12440898	1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12441580	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12443028	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12443486	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16976721	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16976722	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16976737	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16976776	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16976787	1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16976793	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16976808	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16976820	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16976824	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2718927	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28895323	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4310793	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56798454	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7180561	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7181011	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2761872	chr15:56211065-56426501	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv833018	chr15:56325799-56492535	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1045906	chr15:56333180-56473614	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking 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

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56388800-56418400	Weak transcription	Brain Cingulate Gyrus	brain
2	chr15:56388800-56433000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr15:56388800-56437200	Weak transcription	Pancreas	Pancrea
4	chr15:56388800-56441600	Weak transcription	Lung	lung
5	chr15:56389400-56418400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr15:56389400-56418400	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr15:56390600-56418000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr15:56390800-56418600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr15:56394000-56418200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr15:56395000-56418200	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr15:56408000-56418200	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr15:56409400-56418400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr15:56410800-56419400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr15:56411400-56424000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr15:56411600-56436800	Weak transcription	Stomach Smooth Muscle	stomach
16	chr15:56411800-56418600	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr15:56411800-56419600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr15:56412000-56418200	Weak transcription	Gastric	stomach
19	chr15:56412200-56420400	Weak transcription	Colonic Mucosa	Colon
20	chr15:56412400-56423200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
21	chr15:56412600-56419600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr15:56412600-56422000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr15:56412800-56418400	Weak transcription	Psoas Muscle	Psoas
24	chr15:56413200-56423800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
25	chr15:56413400-56418600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr15:56413400-56419400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
27	chr15:56413400-56441600	Weak transcription	Spleen	Spleen
28	chr15:56413600-56421800	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr15:56413800-56418400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr15:56413800-56418400	Weak transcription	Colon Smooth Muscle	Colon
31	chr15:56414000-56418400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr15:56414000-56418600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr15:56414000-56419200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr15:56414200-56419000	Weak transcription	Osteobl	bone
35	chr15:56414200-56419400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr15:56414400-56418000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr15:56414400-56418400	Strong transcription	Liver	Liver
38	chr15:56414400-56418400	Strong transcription	Dnd41	blood
39	chr15:56414400-56419200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr15:56414600-56418200	Strong transcription	Primary B cells from peripheral blood	blood
41	chr15:56414600-56418200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr15:56414800-56418200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr15:56414800-56418400	Weak transcription	Esophagus	oesophagus
44	chr15:56415000-56418600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr15:56415600-56418200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr15:56415800-56418200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr15:56416000-56418000	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr15:56416000-56419400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr15:56416000-56421400	Weak transcription	Placenta	Placenta
50	chr15:56416000-56433200	Weak transcription	Hela-S3	cervix

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