Variant report

Variant	rs984707
Chromosome Location	chr2:40596632-40596633
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10165478	0.92[ASN][1000 genomes]
rs10168748	0.85[CHB][hapmap]
rs10171704	0.94[ASN][1000 genomes]
rs10177941	0.90[ASN][1000 genomes]
rs10178405	0.95[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs10181006	0.83[ASN][1000 genomes]
rs10181007	0.91[ASN][1000 genomes]
rs10189274	0.92[ASN][1000 genomes]
rs10192458	0.92[ASN][1000 genomes]
rs10192546	0.81[CHB][hapmap]
rs10490051	0.95[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap]
rs11690171	0.81[CHB][hapmap]
rs11691852	0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12471797	0.90[ASN][1000 genomes]
rs12613022	0.81[ASN][1000 genomes]
rs12987979	0.81[CHB][hapmap]
rs12988856	0.81[CHB][hapmap]
rs12989200	0.85[CHB][hapmap]
rs12989852	0.81[CHB][hapmap]
rs12995004	0.81[CHB][hapmap]
rs12996962	0.95[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs13014950	0.81[CHB][hapmap]
rs13017968	1.00[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs13022231	0.95[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap]
rs13031340	1.00[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs13031441	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs13032770	0.95[CHB][hapmap];0.87[JPT][hapmap]
rs13405065	0.81[CHB][hapmap]
rs1477002	0.92[ASN][1000 genomes]
rs1477004	0.95[CHB][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs1477005	0.94[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1861293	0.94[ASN][1000 genomes]
rs2192773	0.86[ASN][1000 genomes]
rs2192776	0.91[ASN][1000 genomes]
rs2192779	0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.97[ASN][1000 genomes]
rs2373857	0.95[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];0.88[JPT][hapmap];0.96[MEX][hapmap];0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2373859	0.81[CHB][hapmap];0.87[CHD][hapmap];0.83[ASN][1000 genomes]
rs2888676	0.95[ASN][1000 genomes]
rs4446101	0.90[CHB][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs4452199	0.91[ASN][1000 genomes]
rs4452200	0.92[ASN][1000 genomes]
rs4552227	0.91[ASN][1000 genomes]
rs4588235	0.91[ASN][1000 genomes]
rs4645043	0.95[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs4952409	0.90[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6544323	0.81[CHB][hapmap]
rs6544324	0.86[CHB][hapmap]
rs6544330	0.86[CHB][hapmap]
rs6544333	0.88[ASN][1000 genomes]
rs6544334	0.87[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6718322	0.92[ASN][1000 genomes]
rs6738580	0.86[CHB][hapmap]
rs6738673	0.81[CHB][hapmap]
rs6745881	0.83[ASN][1000 genomes]
rs6747285	0.94[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7424049	0.94[ASN][1000 genomes]
rs7574340	0.89[ASN][1000 genomes]
rs7594786	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7598561	0.82[ASN][1000 genomes]
rs7599953	0.92[ASN][1000 genomes]
rs918002	0.90[ASN][1000 genomes]
rs9309055	0.94[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs967351	0.90[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs981739	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs990270	0.81[CHB][hapmap]

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	nsv529606	chr2:40206280-40896881	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv873911	chr2:40423454-41161464	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv2757794	chr2:40547947-40733776	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv2759044	chr2:40547947-40733776	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv873915	chr2:40573350-40615520	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs984707	EML4	cis	parietal	SCAN
rs984707	GALM	cis	parietal	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40591000-40598400	Weak transcription	Fetal Stomach	stomach
2	chr2:40591600-40600800	Weak transcription	Psoas Muscle	Psoas
3	chr2:40592200-40598000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr2:40592200-40598400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr2:40592200-40598800	Weak transcription	Left Ventricle	heart
6	chr2:40592400-40597200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr2:40592400-40597400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr2:40592400-40597400	Weak transcription	Stomach Smooth Muscle	stomach
9	chr2:40592400-40598000	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr2:40592400-40598000	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr2:40592400-40598400	Weak transcription	Brain Anterior Caudate	brain
12	chr2:40592400-40598400	Weak transcription	Fetal Kidney	kidney
13	chr2:40592400-40598600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr2:40592400-40598800	Weak transcription	Ovary	ovary
15	chr2:40592400-40605200	Weak transcription	Right Atrium	heart
16	chr2:40592800-40597200	Weak transcription	NHDF-Ad	bronchial
17	chr2:40592800-40606600	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr2:40593400-40607000	Weak transcription	Dnd41	blood
19	chr2:40594200-40605200	Weak transcription	Fetal Brain Female	brain
20	chr2:40595000-40598400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr2:40595000-40598800	Weak transcription	Fetal Brain Male	brain
22	chr2:40595000-40611000	Weak transcription	Right Ventricle	heart
23	chr2:40595200-40597000	Weak transcription	HMEC	breast
24	chr2:40595200-40597000	Weak transcription	HSMMtube	muscle
25	chr2:40595200-40597200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr2:40595200-40598400	Weak transcription	Hela-S3	cervix
27	chr2:40596000-40601600	Enhancers	Colon Smooth Muscle	Colon
28	chr2:40596400-40597000	Genic enhancers	Fetal Heart	heart
29	chr2:40596400-40597000	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr2:40596400-40597400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr2:40596400-40598400	Enhancers	Muscle Satellite Cultured Cells	--
32	chr2:40596400-40598800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr2:40596400-40600400	Enhancers	HSMM	muscle
34	chr2:40596400-40601200	Enhancers	Rectal Smooth Muscle	rectum
35	chr2:40596400-40601400	Enhancers	Osteobl	bone
36	chr2:40596600-40598600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr2:40596600-40599800	Enhancers	NH-A	brain

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