Variant report

Variant	rs34408472
Chromosome Location	chr2:40592311-40592312
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11678256	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11687700	0.86[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs11886400	0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11890040	0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12469017	0.82[ASN][1000 genomes]
rs12472012	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs12472064	0.83[ASN][1000 genomes]
rs12615002	0.88[GIH][hapmap];0.82[JPT][hapmap]
rs17025877	0.93[CHD][hapmap];1.00[JPT][hapmap]
rs61578092	0.83[ASN][1000 genomes]
rs6544331	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6724743	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs72939976	0.96[ASN][1000 genomes]
rs72939984	0.92[ASN][1000 genomes]
rs7557545	0.85[CHB][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap];0.85[MEX][hapmap]
rs7570435	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
rs34408472	KCNG3	cis	parietal	SCAN
rs34408472	ABCG8	cis	parietal	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40586800-40593800	Enhancers	Fetal Heart	heart
2	chr2:40590400-40592400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr2:40590400-40592400	Active TSS	Right Atrium	heart
4	chr2:40590600-40592400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr2:40590600-40592400	Active TSS	Aorta	Aorta
6	chr2:40591000-40598400	Weak transcription	Fetal Stomach	stomach
7	chr2:40591600-40592400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr2:40591600-40592400	Active TSS	Ovary	ovary
9	chr2:40591600-40592800	Enhancers	Brain Angular Gyrus	brain
10	chr2:40591600-40600800	Weak transcription	Psoas Muscle	Psoas
11	chr2:40591800-40592400	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr2:40591800-40592400	Enhancers	Brain Anterior Caudate	brain
13	chr2:40591800-40592400	Active TSS	HSMMtube	muscle
14	chr2:40591800-40592400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
15	chr2:40591800-40592600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr2:40591800-40593400	Enhancers	Dnd41	blood
17	chr2:40592000-40592400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr2:40592000-40592400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr2:40592000-40592400	Enhancers	Fetal Kidney	kidney
20	chr2:40592000-40592400	Flanking Active TSS	HUVEC	blood vessel
21	chr2:40592000-40592600	Enhancers	Fetal Brain Female	brain
22	chr2:40592200-40592400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr2:40592200-40592400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr2:40592200-40592400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr2:40592200-40592400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr2:40592200-40592400	Enhancers	Duodenum Smooth Muscle	Duodenum
27	chr2:40592200-40592400	Enhancers	Pancreatic Islets	Pancreatic Islet
28	chr2:40592200-40592400	Flanking Active TSS	Stomach Smooth Muscle	stomach
29	chr2:40592200-40592600	Enhancers	HSMM	muscle
30	chr2:40592200-40592800	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr2:40592200-40592800	Enhancers	Primary hematopoietic stem cells	blood
32	chr2:40592200-40592800	Enhancers	Muscle Satellite Cultured Cells	--
33	chr2:40592200-40592800	Enhancers	Duodenum Mucosa	Duodenum
34	chr2:40592200-40592800	Enhancers	Rectal Smooth Muscle	rectum
35	chr2:40592200-40592800	Flanking Active TSS	NHDF-Ad	bronchial
36	chr2:40592200-40593000	Enhancers	Hela-S3	cervix
37	chr2:40592200-40593000	Enhancers	Osteobl	bone
38	chr2:40592200-40593400	Weak transcription	Fetal Brain Male	brain
39	chr2:40592200-40594200	Enhancers	Colon Smooth Muscle	Colon
40	chr2:40592200-40594200	Weak transcription	NH-A	brain
41	chr2:40592200-40594600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr2:40592200-40594600	Weak transcription	HMEC	breast
43	chr2:40592200-40598000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr2:40592200-40598400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr2:40592200-40598800	Weak transcription	Left Ventricle	heart

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