Variant report

Variant	rs2780142
Chromosome Location	chr9:86461989-86461990
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10124390	0.87[CHB][hapmap]
rs10868051	0.83[EUR][1000 genomes]
rs10868055	0.82[EUR][1000 genomes]
rs10868058	0.85[CEU][hapmap];0.91[CHB][hapmap]
rs10868077	0.82[CHB][hapmap]
rs10868079	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs11140240	0.81[CEU][hapmap];0.96[CHB][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes]
rs11792634	0.88[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.88[EUR][1000 genomes]
rs12349272	0.89[CEU][hapmap];0.96[CHB][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes]
rs12551039	0.83[CHB][hapmap]
rs1572030	0.87[CHB][hapmap]
rs1572031	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs192705	0.80[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap]
rs2065516	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs295270	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs295274	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs295275	0.93[ASN][1000 genomes]
rs295279	0.87[EUR][1000 genomes]
rs295288	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs295291	0.89[CEU][hapmap];0.96[CHB][hapmap];0.86[JPT][hapmap];0.87[EUR][1000 genomes]
rs296885	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs296891	0.87[CHB][hapmap]
rs296892	0.83[CHB][hapmap]
rs427314	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4297107	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes]
rs4877803	0.81[EUR][1000 genomes]
rs4877815	0.83[CHB][hapmap]
rs6559750	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6559754	0.87[CHB][hapmap]
rs6559756	0.83[CHB][hapmap]
rs7020920	0.82[EUR][1000 genomes]
rs7021189	0.83[CHB][hapmap]
rs7026436	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs72749110	0.88[EUR][1000 genomes]
rs754144	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs7851636	0.88[EUR][1000 genomes]
rs7855503	0.89[CEU][hapmap];0.96[CHB][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes]
rs7869387	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7875011	0.83[CHB][hapmap]
rs7875289	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs796001	0.83[CHB][hapmap]
rs9314723	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469859	chr9:86398152-86587957	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv482641	chr9:86398152-86587957	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	esv2758192	chr9:86414024-86603602	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	esv2759701	chr9:86414024-86603602	Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
5	nsv982312	chr9:86424154-86490046	Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv6590	chr9:86435603-86480442	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv8540	chr9:86458587-86470369	Strong transcription ZNF genes & repeats Weak transcription Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
8	esv3440485	chr9:86461957-86464705	Weak transcription Strong transcription Active TSS ZNF genes & repeats	TF binding region lncRNA	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86447800-86470800	Weak transcription	Brain Germinal Matrix	brain
2	chr9:86452000-86467800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr9:86452200-86464000	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr9:86456000-86463600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr9:86456200-86466200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr9:86456600-86472600	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr9:86456800-86463200	Weak transcription	Brain Cingulate Gyrus	brain
8	chr9:86457000-86464000	Weak transcription	Left Ventricle	heart
9	chr9:86457400-86464200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr9:86457400-86468400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr9:86457400-86469000	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr9:86457600-86464000	Weak transcription	Pancreas	Pancrea
13	chr9:86458000-86463600	Weak transcription	Esophagus	oesophagus
14	chr9:86458600-86462800	Strong transcription	Fetal Stomach	stomach
15	chr9:86459600-86464000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr9:86459800-86464200	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr9:86459800-86466400	Weak transcription	Stomach Smooth Muscle	stomach
18	chr9:86460000-86474000	Weak transcription	Adipose Nuclei	Adipose
19	chr9:86460200-86463800	Weak transcription	Right Ventricle	heart
20	chr9:86460400-86462800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr9:86460400-86465400	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr9:86460600-86462800	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr9:86460600-86462800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr9:86460600-86462800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr9:86460600-86462800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr9:86460600-86462800	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr9:86460600-86463000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr9:86460600-86463000	Weak transcription	Primary B cells from cord blood	blood
29	chr9:86460600-86463200	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr9:86460600-86465400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr9:86460600-86518200	Weak transcription	Thymus	Thymus
32	chr9:86460800-86462200	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr9:86460800-86462600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr9:86460800-86463200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr9:86461000-86462600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr9:86461200-86462000	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr9:86461200-86462000	Strong transcription	Spleen	Spleen
38	chr9:86461200-86462200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr9:86461200-86462200	Strong transcription	Liver	Liver
40	chr9:86461200-86462200	Strong transcription	Fetal Brain Female	brain
41	chr9:86461200-86462200	Strong transcription	Fetal Muscle Leg	muscle
42	chr9:86461200-86462200	Strong transcription	Lung	lung
43	chr9:86461200-86462400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr9:86461200-86462600	Strong transcription	Primary T cells from cord blood	blood
45	chr9:86461200-86462600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr9:86461200-86462600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr9:86461200-86462600	Strong transcription	Brain Angular Gyrus	brain
48	chr9:86461200-86462600	Strong transcription	Brain Anterior Caudate	brain
49	chr9:86461200-86462600	Strong transcription	Duodenum Mucosa	Duodenum
50	chr9:86461200-86462600	Strong transcription	Fetal Kidney	kidney

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