Variant report

Variant	rs12237139
Chromosome Location	chr9:96412092-96412093
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:96355442..96358084-chr9:96410672..96413121,3	MCF-7	breast:
2	chr9:96411800..96413942-chr9:96415397..96417041,2	K562	blood:
3	chr9:96405323..96407093-chr9:96410616..96412899,2	K562	blood:
4	chr9:96405323..96407583-chr9:96410616..96412899,3	K562	blood:

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10114689	0.90[CHB][hapmap]
rs10116955	0.90[CHB][hapmap]
rs10122030	0.89[CHB][hapmap]
rs10992808	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10992809	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10992811	1.00[CHB][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10992814	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10992816	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10992821	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10992824	1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10992826	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992827	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992830	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992833	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992834	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992838	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992845	0.86[CHB][hapmap]
rs10992862	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12235863	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];1.00[ASN][1000 genomes]
rs12237261	1.00[EUR][1000 genomes]
rs12238477	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16912647	1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1806673	1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2150752	0.89[CHB][hapmap]
rs2398852	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3750353	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3750356	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];1.00[ASN][1000 genomes]
rs3750360	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];1.00[ASN][1000 genomes]
rs7040568	0.89[CHB][hapmap]
rs7041943	0.90[CHB][hapmap]
rs928369	0.90[CHB][hapmap]
rs9644970	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893586	chr9:96363859-96493773	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
2	nsv1036609	chr9:96375217-96477641	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	nsv893587	chr9:96383605-96451784	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	esv3389059	chr9:96410731-96413929	Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	esv3445482	chr9:96410831-96413929	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96384600-96412200	Weak transcription	Stomach Mucosa	stomach
2	chr9:96392200-96423600	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr9:96398200-96413800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr9:96399000-96423400	Strong transcription	Fetal Intestine Large	intestine
5	chr9:96399400-96423600	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr9:96400400-96430600	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr9:96401000-96430000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr9:96401000-96438600	Weak transcription	Psoas Muscle	Psoas
9	chr9:96401600-96423400	Strong transcription	Adipose Nuclei	Adipose
10	chr9:96401800-96423400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr9:96402600-96430200	Strong transcription	Cortex derived primary cultured neurospheres	brain
12	chr9:96402600-96433600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr9:96403200-96423000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr9:96403400-96430800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr9:96403400-96430800	Strong transcription	Liver	Liver
16	chr9:96403800-96412600	Strong transcription	Placenta	Placenta
17	chr9:96404200-96422600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr9:96405000-96423400	Strong transcription	Fetal Thymus	thymus
19	chr9:96405000-96423800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr9:96405200-96423600	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr9:96405200-96429200	Strong transcription	Duodenum Mucosa	Duodenum
22	chr9:96405200-96431400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr9:96405400-96423000	Strong transcription	Fetal Stomach	stomach
24	chr9:96405400-96423200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr9:96405400-96423200	Strong transcription	Thymus	Thymus
26	chr9:96405400-96423400	Strong transcription	Brain Angular Gyrus	brain
27	chr9:96405400-96423400	Strong transcription	Dnd41	blood
28	chr9:96405400-96423600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr9:96405400-96423600	Strong transcription	Brain Inferior Temporal Lobe	brain
30	chr9:96405400-96430000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr9:96405400-96430600	Strong transcription	Primary T cells from cord blood	blood
32	chr9:96405400-96431400	Strong transcription	Fetal Brain Female	brain
33	chr9:96405400-96433200	Strong transcription	Fetal Intestine Small	intestine
34	chr9:96405600-96412200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr9:96405600-96414200	Strong transcription	Aorta	Aorta
36	chr9:96405600-96423200	Strong transcription	Sigmoid Colon	Sigmoid Colon
37	chr9:96405600-96423400	Strong transcription	Brain Cingulate Gyrus	brain
38	chr9:96405600-96423400	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr9:96405600-96429800	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr9:96405600-96430000	Strong transcription	Brain Germinal Matrix	brain
41	chr9:96405600-96430400	Strong transcription	Stomach Smooth Muscle	stomach
42	chr9:96405800-96412200	Strong transcription	Right Ventricle	heart
43	chr9:96405800-96415800	Strong transcription	Left Ventricle	heart
44	chr9:96405800-96417400	Strong transcription	Brain Anterior Caudate	brain
45	chr9:96405800-96423200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr9:96405800-96423600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr9:96405800-96423800	Strong transcription	Ovary	ovary
48	chr9:96406000-96423200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr9:96406200-96438600	Weak transcription	Small Intestine	intestine
50	chr9:96406600-96423600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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