Variant report

Variant	rs2710637
Chromosome Location	chr2:63173450-63173451
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10153716	0.84[ASN][1000 genomes]
rs1022110	0.92[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11682530	0.92[CEU][hapmap];0.86[GIH][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs11893131	0.87[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12713468	0.83[CEU][hapmap]
rs12989754	0.85[ASW][hapmap];0.87[CEU][hapmap];0.87[GIH][hapmap];0.91[TSI][hapmap];0.83[YRI][hapmap]
rs13013218	0.85[ASW][hapmap];0.87[CEU][hapmap];0.87[GIH][hapmap];0.89[TSI][hapmap]
rs13410889	0.95[CHD][hapmap]
rs13418889	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1420018	0.91[CEU][hapmap];0.93[EUR][1000 genomes]
rs1468748	0.85[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1553832	0.83[CEU][hapmap]
rs17027429	0.92[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1828398	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1877026	0.82[CHD][hapmap]
rs2058566	0.96[CEU][hapmap];0.93[GIH][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes]
rs2058567	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2075375	0.91[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap]
rs2080227	0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs2215870	0.87[CEU][hapmap];0.87[GIH][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs2421816	0.96[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2430386	0.84[ASN][1000 genomes]
rs2430388	0.92[ASW][hapmap];0.87[CEU][hapmap];0.87[GIH][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.90[EUR][1000 genomes]
rs2539978	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.89[TSI][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2539980	0.92[CEU][hapmap];0.87[GIH][hapmap];0.85[EUR][1000 genomes]
rs2539984	0.96[ASN][1000 genomes]
rs2539985	0.90[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs2539987	0.92[ASW][hapmap];0.87[CEU][hapmap];0.87[GIH][hapmap];0.91[TSI][hapmap]
rs2539990	0.86[ASN][1000 genomes]
rs2710639	0.92[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2710640	0.92[EUR][1000 genomes]
rs2710642	0.96[CEU][hapmap];0.90[GIH][hapmap];0.98[TSI][hapmap];0.93[EUR][1000 genomes]
rs2710651	0.84[ASN][1000 genomes]
rs34104251	0.81[ASN][1000 genomes]
rs4461246	0.85[ASW][hapmap];0.87[CEU][hapmap];0.87[GIH][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs4671050	0.87[CEU][hapmap];0.87[GIH][hapmap]
rs4671051	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6545971	0.91[CEU][hapmap];0.86[YRI][hapmap];0.89[EUR][1000 genomes]
rs6545972	0.92[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6545973	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6705798	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs6714241	0.86[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs6739804	0.91[CEU][hapmap];0.87[GIH][hapmap];0.82[TSI][hapmap]
rs7557501	0.92[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7562149	0.85[ASW][hapmap];0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.88[TSI][hapmap];0.83[YRI][hapmap];0.84[ASN][1000 genomes]
rs7562734	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7567923	0.92[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7571916	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7573756	0.83[CEU][hapmap];0.87[GIH][hapmap]
rs7591708	0.89[CHD][hapmap];0.81[JPT][hapmap]
rs9789661	0.82[EUR][1000 genomes]
rs9973612	0.87[CEU][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv535767	chr2:62461582-63413596	Bivalent Enhancer Strong transcription Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	esv3417336	chr2:62957866-63749654	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv428041	chr2:63027947-63206574	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1006848	chr2:63061816-63631407	Weak transcription Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	esv2756598	chr2:63085848-63491438	Strong transcription Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	esv3340700	chr2:63127412-63534998	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2710637	VPS54	cis	cerebellum	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:63142400-63190800	Weak transcription	Brain Angular Gyrus	brain
2	chr2:63150600-63176000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr2:63151200-63175600	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr2:63151200-63182800	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr2:63151400-63194200	Weak transcription	Esophagus	oesophagus
6	chr2:63151400-63194200	Weak transcription	Fetal Brain Male	brain
7	chr2:63151400-63200800	Weak transcription	Fetal Stomach	stomach
8	chr2:63151400-63208800	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr2:63151400-63272200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr2:63152200-63175600	Weak transcription	Primary T cells from cord blood	blood
11	chr2:63154400-63209000	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr2:63155400-63209000	Weak transcription	Psoas Muscle	Psoas
13	chr2:63157400-63175600	Weak transcription	Left Ventricle	heart
14	chr2:63157400-63188800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr2:63157400-63207400	Weak transcription	Pancreas	Pancrea
16	chr2:63160200-63190000	Weak transcription	Primary B cells from cord blood	blood
17	chr2:63161800-63184400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr2:63162000-63196800	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr2:63162000-63199800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr2:63165200-63209200	Weak transcription	Aorta	Aorta
21	chr2:63167000-63194000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr2:63167400-63175400	Weak transcription	NH-A	brain
23	chr2:63167400-63200800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr2:63167400-63206400	Weak transcription	Colon Smooth Muscle	Colon
25	chr2:63167600-63173600	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr2:63167600-63174000	Weak transcription	HSMM	muscle
27	chr2:63167600-63181800	Weak transcription	HMEC	breast
28	chr2:63167600-63187400	Weak transcription	NHLF	lung
29	chr2:63167600-63206200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr2:63167600-63256000	Weak transcription	HSMMtube	muscle
31	chr2:63167800-63173600	Weak transcription	NHEK	skin
32	chr2:63167800-63175400	Weak transcription	Osteobl	bone
33	chr2:63167800-63225800	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr2:63168200-63220200	Weak transcription	Rectal Smooth Muscle	rectum
35	chr2:63168400-63182600	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr2:63168400-63187600	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr2:63168800-63174800	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr2:63168800-63194000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr2:63169000-63178000	Weak transcription	Fetal Intestine Large	intestine
40	chr2:63169200-63181400	Strong transcription	HepG2	liver
41	chr2:63169200-63185000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr2:63169200-63206200	Weak transcription	Fetal Muscle Trunk	muscle
43	chr2:63169200-63206600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr2:63169400-63179400	Strong transcription	NHDF-Ad	bronchial
45	chr2:63169400-63196400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr2:63169600-63175600	Weak transcription	Fetal Muscle Leg	muscle
47	chr2:63169600-63180200	Strong transcription	Liver	Liver
48	chr2:63169600-63182600	Weak transcription	Placenta	Placenta
49	chr2:63169600-63182600	Weak transcription	Dnd41	blood
50	chr2:63169600-63228800	Weak transcription	GM12878-XiMat	blood

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