Variant report

Variant	rs12001366
Chromosome Location	chr9:93622150-93622151
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:93571707..93573621-chr9:93620166..93622474,2	MCF-7	breast:
2	chr9:93619506..93622175-chr9:93629106..93631175,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10124093	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10512203	1.00[GIH][hapmap]
rs10993722	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10993723	0.93[CHB][hapmap];0.88[JPT][hapmap];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10993724	0.93[CHB][hapmap];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10993725	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10993727	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[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993728	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10993729	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12000793	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12003597	0.84[CHD][hapmap];1.00[GIH][hapmap]
rs12006330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1572104	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs16906923	0.84[CHD][hapmap];1.00[GIH][hapmap]
rs2290885	0.84[CHD][hapmap];1.00[GIH][hapmap]
rs2290887	0.84[CHD][hapmap];1.00[GIH][hapmap]
rs2290890	0.87[CHD][hapmap];1.00[GIH][hapmap]
rs2290891	0.87[CHD][hapmap];1.00[GIH][hapmap]
rs2306040	1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2306041	0.84[CHD][hapmap];1.00[GIH][hapmap]
rs35478826	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs36063880	0.98[ASN][1000 genomes]
rs3789902	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3789903	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3789909	0.82[EUR][1000 genomes]
rs4529574	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4744019	0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap]
rs4744516	0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4744517	0.82[AMR][1000 genomes]
rs7866696	1.00[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046989	chr9:93353987-93800416	Transcr. at gene 5' and 3' Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv831652	chr9:93527411-93696923	Bivalent Enhancer Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv893568	chr9:93539879-93774385	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv1038685	chr9:93556174-93685729	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1039761	chr9:93598856-93677831	Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1039326	chr9:93598856-93685729	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv430078	chr9:93609668-93642766	Strong transcription Weak transcription Genic enhancers Enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv1053252	chr9:93610132-93699103	Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv430079	chr9:93620963-93642766	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:93601800-93642200	Weak transcription	Rectal Smooth Muscle	rectum
2	chr9:93605000-93622800	Weak transcription	Adipose Nuclei	Adipose
3	chr9:93605000-93633000	Weak transcription	Fetal Kidney	kidney
4	chr9:93605800-93631000	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr9:93608200-93624400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr9:93610400-93624600	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr9:93611200-93642200	Weak transcription	Stomach Mucosa	stomach
8	chr9:93612400-93623200	Weak transcription	Colonic Mucosa	Colon
9	chr9:93614800-93623800	Weak transcription	Left Ventricle	heart
10	chr9:93615400-93624000	Weak transcription	Gastric	stomach
11	chr9:93615600-93623200	Weak transcription	Esophagus	oesophagus
12	chr9:93615600-93623600	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr9:93616800-93624400	Weak transcription	Lung	lung
14	chr9:93617200-93624000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr9:93617200-93640600	Weak transcription	K562	blood
16	chr9:93617400-93622600	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr9:93617400-93622800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr9:93617400-93629600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr9:93617400-93640600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr9:93617600-93623400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr9:93617800-93640600	Weak transcription	NHEK	skin
22	chr9:93619000-93623800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr9:93619200-93623600	Genic enhancers	Primary B cells from peripheral blood	blood
24	chr9:93619400-93630000	Strong transcription	Thymus	Thymus
25	chr9:93619800-93622200	Strong transcription	Fetal Intestine Large	intestine
26	chr9:93619800-93622800	Weak transcription	GM12878-XiMat	blood
27	chr9:93619800-93627000	Strong transcription	Fetal Intestine Small	intestine
28	chr9:93620200-93623000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr9:93620600-93624000	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr9:93620800-93625600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr9:93621000-93622800	Weak transcription	Fetal Stomach	stomach
32	chr9:93621000-93623200	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr9:93621200-93626600	Strong transcription	Fetal Thymus	thymus
34	chr9:93621200-93631400	Strong transcription	Primary B cells from cord blood	blood
35	chr9:93621400-93623800	Genic enhancers	Monocytes-CD14+_RO01746	blood
36	chr9:93621600-93622600	Genic enhancers	Primary monocytes fromperipheralblood	blood
37	chr9:93621600-93626200	Weak transcription	Primary T cells from cord blood	blood
38	chr9:93621800-93622400	Enhancers	Pancreas	Pancrea
39	chr9:93621800-93623800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
40	chr9:93621800-93623800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr9:93622000-93622600	Enhancers	Spleen	Spleen
42	chr9:93622000-93622800	Strong transcription	Primary hematopoietic stem cells	blood
43	chr9:93622000-93623200	Genic enhancers	Duodenum Mucosa	Duodenum

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