Variant report

Variant	rs12133428
Chromosome Location	chr1:227152392-227152393
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1045247	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs10495259	0.86[AFR][1000 genomes]
rs10495271	0.93[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs10495272	0.87[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs10916079	0.85[EUR][1000 genomes]
rs11583247	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs11583340	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs11586575	0.86[AFR][1000 genomes]
rs11586734	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12117207	0.91[CEU][hapmap];0.84[JPT][hapmap]
rs12122759	0.93[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12127665	0.86[AFR][1000 genomes]
rs12128667	0.86[AFR][1000 genomes]
rs12131913	0.93[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs12136857	0.86[AFR][1000 genomes]
rs12739480	0.86[CEU][hapmap]
rs12744825	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs12751015	0.93[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs1316850	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1320495	0.93[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs17544956	0.86[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs17545704	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs17592190	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17601316	0.83[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs17601919	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs17602169	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2150874	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2777834	0.81[CEU][hapmap]
rs2802275	0.82[CEU][hapmap]
rs34169114	0.86[AFR][1000 genomes]
rs34556998	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34653494	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35817866	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs3768422	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3768431	0.93[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3820651	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs61836468	0.86[AFR][1000 genomes]
rs6664330	0.86[AFR][1000 genomes]
rs6681959	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs6695431	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6698156	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7526822	0.93[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs7538237	0.81[EUR][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	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv873236	chr1:227118912-227173537	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv873237	chr1:227118912-227178948	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv873238	chr1:227118912-227180858	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv520923	chr1:227127618-227178948	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227129000-227162600	Weak transcription	Fetal Kidney	kidney
2	chr1:227130400-227154600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr1:227131000-227171800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr1:227131400-227153800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr1:227134400-227153000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:227135200-227152600	Weak transcription	Colonic Mucosa	Colon
7	chr1:227135200-227158000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:227136200-227152800	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr1:227140000-227152800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr1:227140000-227153000	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr1:227142200-227157800	Weak transcription	Fetal Lung	lung
12	chr1:227143000-227153800	Weak transcription	Hela-S3	cervix
13	chr1:227143400-227161200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr1:227145400-227159600	Weak transcription	Brain Substantia Nigra	brain
15	chr1:227146400-227162600	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr1:227146800-227152800	Weak transcription	Primary hematopoietic stem cells	blood
17	chr1:227147000-227177000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr1:227147200-227161000	Weak transcription	Stomach Mucosa	stomach
19	chr1:227147400-227156400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr1:227147800-227158600	Strong transcription	Primary T cells from cord blood	blood
21	chr1:227148200-227153400	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr1:227148200-227162000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:227148400-227153000	Weak transcription	Dnd41	blood
24	chr1:227148400-227156400	Strong transcription	Fetal Intestine Small	intestine
25	chr1:227148400-227156600	Strong transcription	Fetal Stomach	stomach
26	chr1:227148400-227159400	Weak transcription	A549	lung
27	chr1:227148600-227152600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr1:227148600-227158400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr1:227148600-227180800	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr1:227148800-227153400	Weak transcription	Fetal Thymus	thymus
31	chr1:227148800-227153600	Genic enhancers	Pancreas	Pancrea
32	chr1:227149000-227153800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr1:227149000-227157600	Weak transcription	K562	blood
34	chr1:227149000-227158600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr1:227149200-227154800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr1:227149200-227156600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr1:227149200-227158400	Strong transcription	Ovary	ovary
38	chr1:227149400-227155200	Strong transcription	Gastric	stomach
39	chr1:227149400-227156400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr1:227149400-227158400	Strong transcription	Rectal Mucosa Donor 29	rectum
41	chr1:227149400-227161600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr1:227149800-227153000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr1:227149800-227154600	Strong transcription	Esophagus	oesophagus
44	chr1:227149800-227155400	Strong transcription	Sigmoid Colon	Sigmoid Colon
45	chr1:227150000-227152400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
46	chr1:227150000-227155400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr1:227150000-227155800	Genic enhancers	Left Ventricle	heart
48	chr1:227150200-227152400	Genic enhancers	Spleen	Spleen
49	chr1:227150200-227154400	Genic enhancers	Right Ventricle	heart
50	chr1:227150200-227158400	Strong transcription	Duodenum Mucosa	Duodenum

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