Variant report

Variant	rs12402226
Chromosome Location	chr1:57006265-57006266
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10443239	0.88[ASN][1000 genomes]
rs10493211	1.00[JPT][hapmap]
rs10789026	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10888978	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11206831	1.00[JPT][hapmap]
rs11206832	1.00[JPT][hapmap]
rs11206834	0.88[ASN][1000 genomes]
rs11206835	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11206838	1.00[JPT][hapmap]
rs11576602	1.00[JPT][hapmap]
rs11582172	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12134109	1.00[JPT][hapmap]
rs12406517	1.00[JPT][hapmap]
rs1572057	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs17470134	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs1930759	1.00[YRI][hapmap]
rs2404717	0.88[ASN][1000 genomes]
rs3738570	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs3927762	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7528118	1.00[JPT][hapmap]
rs7551402	1.00[JPT][hapmap]
rs8016	1.00[JPT][hapmap]
rs869934	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869295	chr1:56894955-57656562	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:56987000-57015000	Genic enhancers	NHDF-Ad	bronchial
2	chr1:56992800-57011200	Weak transcription	Stomach Mucosa	stomach
3	chr1:56993600-57007800	Weak transcription	Primary B cells from cord blood	blood
4	chr1:56994000-57012400	Weak transcription	Fetal Brain Male	brain
5	chr1:56994000-57012800	Weak transcription	Fetal Brain Female	brain
6	chr1:56999400-57012800	Weak transcription	HSMMtube	muscle
7	chr1:57000200-57008200	Weak transcription	Fetal Kidney	kidney
8	chr1:57000400-57011000	Weak transcription	Gastric	stomach
9	chr1:57000400-57013000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:57001200-57018800	Weak transcription	A549	lung
11	chr1:57001800-57018600	Weak transcription	Small Intestine	intestine
12	chr1:57001800-57021800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr1:57002400-57008600	Enhancers	Brain Hippocampus Middle	brain
14	chr1:57002600-57006600	Enhancers	Right Atrium	heart
15	chr1:57002600-57008600	Enhancers	Brain Anterior Caudate	brain
16	chr1:57002800-57006400	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr1:57002800-57006600	Enhancers	H9 Cell Line	embryonic stem cell
18	chr1:57002800-57006800	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr1:57002800-57006800	Enhancers	Fetal Intestine Small	intestine
20	chr1:57002800-57013200	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr1:57002800-57018600	Weak transcription	Thymus	Thymus
22	chr1:57003000-57006800	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr1:57003000-57006800	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr1:57003000-57007200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr1:57003000-57007600	Enhancers	Adipose Nuclei	Adipose
26	chr1:57003000-57008000	Enhancers	HUES64 Cell Line	embryonic stem cell
27	chr1:57003000-57008600	Enhancers	H1 Cell Line	embryonic stem cell
28	chr1:57003200-57007600	Enhancers	Brain Substantia Nigra	brain
29	chr1:57003200-57007600	Enhancers	Fetal Lung	lung
30	chr1:57003200-57011400	Weak transcription	Lung	lung
31	chr1:57003200-57019800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr1:57003400-57008600	Enhancers	Ovary	ovary
33	chr1:57003400-57015400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr1:57003600-57007600	Enhancers	Brain Cingulate Gyrus	brain
35	chr1:57003600-57013200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr1:57003800-57006400	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr1:57003800-57007800	Weak transcription	Fetal Muscle Trunk	muscle
38	chr1:57003800-57011200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr1:57004000-57007800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr1:57004000-57007800	Weak transcription	HSMM	muscle
41	chr1:57004000-57008000	Enhancers	HepG2	liver
42	chr1:57004000-57008200	Enhancers	Cortex derived primary cultured neurospheres	brain
43	chr1:57004000-57011200	Weak transcription	Spleen	Spleen
44	chr1:57004000-57014800	Weak transcription	Fetal Thymus	thymus
45	chr1:57004200-57006800	Enhancers	Duodenum Smooth Muscle	Duodenum
46	chr1:57004200-57007000	Enhancers	Fetal Stomach	stomach
47	chr1:57004200-57011400	Weak transcription	Esophagus	oesophagus
48	chr1:57004400-57013200	Weak transcription	Duodenum Mucosa	Duodenum
49	chr1:57004600-57006400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr1:57004600-57007600	Weak transcription	Placenta	Placenta

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