Variant report

Variant	rs3180887
Chromosome Location	chr9:86553589-86553590
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10114889	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap]
rs10124390	0.82[LWK][hapmap]
rs10868071	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs10868076	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11140251	0.81[CHB][hapmap]
rs11140253	0.81[CHB][hapmap]
rs11140265	0.87[CHB][hapmap];0.92[JPT][hapmap]
rs11140304	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12378956	0.88[CHB][hapmap];0.92[JPT][hapmap]
rs12682981	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs13290882	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap]
rs13296528	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs167203	0.82[CEU][hapmap]
rs1831757	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs1982151	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap]
rs2378661	0.88[CHB][hapmap];0.92[JPT][hapmap]
rs2576362	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap]
rs2780103	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap]
rs296886	0.82[CEU][hapmap];0.83[TSI][hapmap]
rs296887	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs296888	0.82[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap]
rs296889	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap]
rs296890	0.94[CHB][hapmap];0.92[JPT][hapmap]
rs296891	0.82[LWK][hapmap]
rs296893	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs3818725	0.81[CHB][hapmap]
rs4147132	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap]
rs4147133	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap]
rs4298563	0.88[ASW][hapmap];0.83[MKK][hapmap]
rs4535826	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs6559751	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs6559754	0.82[LWK][hapmap]
rs7020300	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap]
rs7033292	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs7047907	0.94[CEU][hapmap];0.88[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap]
rs7853377	0.82[CEU][hapmap]
rs7869321	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs9410888	0.81[CHB][hapmap]
rs963459	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]

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	nsv8541	chr9:86469723-86593758	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv831644	chr9:86534310-86704395	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
7	esv3366490	chr9:86541369-86608868	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
8	nsv1043703	chr9:86545917-86603545	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3180887	LOC440173	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86536600-86571000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:86537000-86553600	Weak transcription	Fetal Intestine Small	intestine
3	chr9:86537000-86553600	Weak transcription	Thymus	Thymus
4	chr9:86543000-86571000	Weak transcription	Esophagus	oesophagus
5	chr9:86546800-86553600	Weak transcription	Fetal Thymus	thymus
6	chr9:86547200-86553600	Weak transcription	Primary T cells from cord blood	blood
7	chr9:86547200-86553800	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr9:86547200-86570200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr9:86547800-86554200	Weak transcription	Dnd41	blood
10	chr9:86548000-86567000	Weak transcription	GM12878-XiMat	blood
11	chr9:86548800-86554400	Weak transcription	Small Intestine	intestine
12	chr9:86549000-86553800	Weak transcription	Pancreas	Pancrea
13	chr9:86549000-86570200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr9:86549600-86553600	Weak transcription	Liver	Liver
15	chr9:86549600-86553600	Weak transcription	Fetal Stomach	stomach
16	chr9:86549600-86553600	Weak transcription	Left Ventricle	heart
17	chr9:86549600-86557000	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr9:86550200-86553600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr9:86550200-86553600	Weak transcription	Colon Smooth Muscle	Colon
20	chr9:86550200-86553800	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr9:86550200-86553800	Weak transcription	Ovary	ovary
22	chr9:86550200-86553800	Weak transcription	Stomach Smooth Muscle	stomach
23	chr9:86550200-86554000	Weak transcription	Lung	lung
24	chr9:86550200-86554000	Weak transcription	Right Ventricle	heart
25	chr9:86550200-86554400	Weak transcription	HSMMtube	muscle
26	chr9:86550200-86555000	Weak transcription	A549	lung
27	chr9:86550200-86555600	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr9:86550200-86557000	Weak transcription	Primary hematopoietic stem cells	blood
29	chr9:86550200-86557200	Weak transcription	Rectal Smooth Muscle	rectum
30	chr9:86550200-86559200	Weak transcription	Brain Anterior Caudate	brain
31	chr9:86550200-86570400	Weak transcription	Aorta	Aorta
32	chr9:86550400-86553600	Weak transcription	Brain Cingulate Gyrus	brain
33	chr9:86550400-86553600	Weak transcription	Fetal Muscle Leg	muscle
34	chr9:86550400-86554200	Weak transcription	Placenta	Placenta
35	chr9:86550400-86569200	Weak transcription	Fetal Heart	heart
36	chr9:86550400-86570400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr9:86550600-86553600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr9:86550600-86553800	Weak transcription	Psoas Muscle	Psoas
39	chr9:86550600-86554000	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr9:86550600-86554200	Weak transcription	Fetal Lung	lung
41	chr9:86550600-86554400	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr9:86550600-86556800	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr9:86550600-86559200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr9:86550600-86569000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr9:86550800-86553600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr9:86550800-86553600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr9:86550800-86555400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr9:86550800-86555600	Weak transcription	Brain Hippocampus Middle	brain
49	chr9:86550800-86556800	Weak transcription	Primary B cells from cord blood	blood
50	chr9:86550800-86558400	Weak transcription	NHLF	lung

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