Variant report

Variant	rs994249
Chromosome Location	chr2:40597273-40597274
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10182686	0.86[EUR][1000 genomes]
rs10187203	0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10208527	0.83[CHB][hapmap]
rs12465380	0.83[CHB][hapmap];0.82[GIH][hapmap]
rs12474472	0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12611608	0.83[CHB][hapmap]
rs13405465	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2216009	0.85[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4395287	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4952410	1.00[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];0.91[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4952614	0.91[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs57686441	0.81[EUR][1000 genomes]
rs6712494	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6712622	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6732915	0.91[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6742210	0.83[CHB][hapmap];0.93[JPT][hapmap];0.91[MEX][hapmap]
rs72939984	0.82[AFR][1000 genomes]
rs7561383	0.83[CHB][hapmap]
rs7581508	0.81[GIH][hapmap];0.92[JPT][hapmap]
rs7581611	0.81[ASW][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.94[MKK][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs918001	1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[JPT][hapmap];0.88[MEX][hapmap];0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9309054	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[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	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
rs994249	EML4	cis	parietal	SCAN
rs994249	PLEKHH2	cis	parietal	SCAN

Chromatin state (count:38 , 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	chr2:40592400-40597400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr2:40592400-40597400	Weak transcription	Stomach Smooth Muscle	stomach
8	chr2:40592400-40598000	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr2:40592400-40598000	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr2:40592400-40598400	Weak transcription	Brain Anterior Caudate	brain
11	chr2:40592400-40598400	Weak transcription	Fetal Kidney	kidney
12	chr2:40592400-40598600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr2:40592400-40598800	Weak transcription	Ovary	ovary
14	chr2:40592400-40605200	Weak transcription	Right Atrium	heart
15	chr2:40592800-40606600	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr2:40593400-40607000	Weak transcription	Dnd41	blood
17	chr2:40594200-40605200	Weak transcription	Fetal Brain Female	brain
18	chr2:40595000-40598400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr2:40595000-40598800	Weak transcription	Fetal Brain Male	brain
20	chr2:40595000-40611000	Weak transcription	Right Ventricle	heart
21	chr2:40595200-40598400	Weak transcription	Hela-S3	cervix
22	chr2:40596000-40601600	Enhancers	Colon Smooth Muscle	Colon
23	chr2:40596400-40597400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr2:40596400-40598400	Enhancers	Muscle Satellite Cultured Cells	--
25	chr2:40596400-40598800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr2:40596400-40600400	Enhancers	HSMM	muscle
27	chr2:40596400-40601200	Enhancers	Rectal Smooth Muscle	rectum
28	chr2:40596400-40601400	Enhancers	Osteobl	bone
29	chr2:40596600-40598600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr2:40596600-40599800	Enhancers	NH-A	brain
31	chr2:40597000-40597600	Enhancers	HMEC	breast
32	chr2:40597000-40598000	Enhancers	Fetal Heart	heart
33	chr2:40597000-40601200	Enhancers	HSMMtube	muscle
34	chr2:40597000-40603400	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr2:40597200-40597400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr2:40597200-40598600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr2:40597200-40599000	Enhancers	NHDF-Ad	bronchial
38	chr2:40597200-40601400	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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