Variant report

Variant	rs2543629
Chromosome Location	chr2:54069947-54069948
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10490468	0.84[CHB][hapmap];0.86[CHD][hapmap];0.86[ASN][1000 genomes]
rs11897282	0.90[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[GIH][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11901698	1.00[CEU][hapmap];0.92[CHB][hapmap];0.82[EUR][1000 genomes]
rs1232	0.80[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.89[JPT][hapmap];0.86[LWK][hapmap];0.87[MKK][hapmap];0.90[ASN][1000 genomes]
rs13408029	0.82[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs17045176	0.92[CHB][hapmap];0.89[ASN][1000 genomes]
rs17045203	0.92[CHB][hapmap];0.82[ASN][1000 genomes]
rs17520505	0.85[CHB][hapmap];0.89[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17521008	0.90[ASW][hapmap];0.93[GIH][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2008082	0.82[EUR][1000 genomes]
rs2287340	0.92[CHB][hapmap];0.81[CHD][hapmap];0.83[ASN][1000 genomes]
rs2302797	0.90[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[GIH][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2542572	0.94[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2542573	0.91[ASN][1000 genomes]
rs2542578	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2542580	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2542581	0.90[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];0.93[MEX][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs2542582	0.85[CHB][hapmap];0.81[ASN][1000 genomes]
rs2542589	0.85[CHB][hapmap];0.89[ASN][1000 genomes]
rs2542590	0.89[ASN][1000 genomes]
rs2542591	0.85[CHB][hapmap];0.89[ASN][1000 genomes]
rs2542592	0.92[CHB][hapmap];0.92[ASN][1000 genomes]
rs2692512	0.93[ASN][1000 genomes]
rs2692513	0.93[ASN][1000 genomes]
rs2692519	0.85[CHB][hapmap];0.88[ASN][1000 genomes]
rs2692521	0.92[ASN][1000 genomes]
rs2692522	0.91[ASN][1000 genomes]
rs2692523	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2692533	0.85[CHB][hapmap];0.81[CHD][hapmap];0.81[ASN][1000 genomes]
rs2692535	0.82[ASN][1000 genomes]
rs2949813	1.00[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs2949814	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs35772199	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3770394	0.92[CHB][hapmap];0.86[ASN][1000 genomes]
rs3770395	0.86[ASN][1000 genomes]
rs3770397	0.89[ASN][1000 genomes]
rs3770399	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3770411	0.81[ASW][hapmap];0.83[CEU][hapmap];0.85[CHB][hapmap]
rs4116709	0.85[CHB][hapmap];0.89[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56214822	0.82[EUR][1000 genomes]
rs62137565	0.82[EUR][1000 genomes]
rs62137573	0.85[ASN][1000 genomes]
rs62137602	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62137606	0.86[ASN][1000 genomes]
rs62137610	0.82[ASN][1000 genomes]
rs62137611	0.82[ASN][1000 genomes]
rs62137612	0.82[ASN][1000 genomes]
rs6730006	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs719127	1.00[CEU][hapmap];0.92[CHB][hapmap];0.89[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72901256	0.88[ASN][1000 genomes]
rs7558968	0.82[EUR][1000 genomes]
rs7583622	0.89[CEU][hapmap]
rs7600817	0.86[ASN][1000 genomes]
rs805316	0.92[CHB][hapmap];0.91[CHD][hapmap];0.89[JPT][hapmap];0.82[LWK][hapmap]
rs805334	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs805338	0.80[CEU][hapmap];0.92[CHB][hapmap];0.89[JPT][hapmap]
rs805368	0.89[ASN][1000 genomes]
rs805383	0.90[ASN][1000 genomes]
rs805385	0.90[ASN][1000 genomes]
rs805398	0.86[ASN][1000 genomes]
rs805413	0.83[ASN][1000 genomes]
rs805435	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs805437	0.92[CHB][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs805446	0.80[CEU][hapmap];0.92[CHB][hapmap];0.89[JPT][hapmap]
rs805447	0.80[CEU][hapmap];0.92[CHB][hapmap];0.89[JPT][hapmap]
rs805449	0.80[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834058	chr2:53900674-54072011	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2543629	RAE1	trans	cerebellum	SCAN
rs2543629	PSME4	cis	cerebellum	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54025800-54085600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr2:54046600-54080200	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr2:54046600-54080200	Weak transcription	NHDF-Ad	bronchial
4	chr2:54046800-54070800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr2:54046800-54080400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr2:54047000-54080200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr2:54047000-54080200	Weak transcription	A549	lung
8	chr2:54047000-54080400	Weak transcription	Gastric	stomach
9	chr2:54047000-54080400	Weak transcription	Pancreas	Pancrea
10	chr2:54047000-54080800	Weak transcription	Aorta	Aorta
11	chr2:54047200-54070800	Weak transcription	Placenta	Placenta
12	chr2:54047200-54077000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr2:54047200-54080000	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr2:54047200-54080200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr2:54047200-54080200	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr2:54047200-54080200	Weak transcription	Fetal Muscle Trunk	muscle
17	chr2:54047200-54080400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr2:54047200-54080400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr2:54047200-54080800	Weak transcription	Primary B cells from peripheral blood	blood
20	chr2:54047600-54080400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr2:54047600-54080800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr2:54050200-54080400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr2:54050400-54080200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr2:54050600-54080200	Weak transcription	Fetal Stomach	stomach
25	chr2:54051000-54080000	Weak transcription	Osteobl	bone
26	chr2:54054000-54080400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr2:54054400-54080400	Weak transcription	NHLF	lung
28	chr2:54055000-54075000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr2:54055200-54075000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr2:54055200-54080400	Weak transcription	Ovary	ovary
31	chr2:54055200-54081000	Weak transcription	Psoas Muscle	Psoas
32	chr2:54055400-54076400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr2:54055400-54080000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr2:54056200-54080200	Weak transcription	Fetal Muscle Leg	muscle
35	chr2:54056800-54080200	Weak transcription	Brain Substantia Nigra	brain
36	chr2:54057200-54070000	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr2:54057200-54080200	Weak transcription	Brain Angular Gyrus	brain
38	chr2:54057200-54080200	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr2:54057200-54080200	Weak transcription	Fetal Brain Female	brain
40	chr2:54057200-54080200	Weak transcription	Left Ventricle	heart
41	chr2:54057400-54080200	Weak transcription	Brain Hippocampus Middle	brain
42	chr2:54057600-54074800	Weak transcription	HepG2	liver
43	chr2:54060000-54080200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr2:54060000-54080200	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr2:54060200-54080200	Weak transcription	Primary T cells from cord blood	blood
46	chr2:54061600-54080200	Weak transcription	Primary B cells from cord blood	blood
47	chr2:54063200-54078200	Weak transcription	Adipose Nuclei	Adipose
48	chr2:54063200-54080000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr2:54063200-54080400	Weak transcription	Esophagus	oesophagus
50	chr2:54063400-54080200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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