Variant report

Variant	rs2539986
Chromosome Location	chr2:63135100-63135101
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:63133462..63135677-chr2:63137317..63139030,2	K562	blood:

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12617178	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12987254	0.84[CEU][hapmap];0.88[GIH][hapmap];0.94[MEX][hapmap];0.93[MKK][hapmap];0.87[AMR][1000 genomes]
rs13030015	0.84[CEU][hapmap];0.90[MKK][hapmap]
rs13398408	0.89[CEU][hapmap];0.82[GIH][hapmap]
rs1362311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.95[MKK][hapmap];0.94[TSI][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2058566	0.81[MKK][hapmap]
rs2160100	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2539979	0.84[ASW][hapmap];1.00[CEU][hapmap];0.82[GIH][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs2553042	0.84[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[LWK][hapmap];0.88[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs2710636	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2710642	0.83[MKK][hapmap]
rs2710648	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes]
rs34503992	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs35499742	0.82[GIH][hapmap]
rs35801289	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs36009942	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs360786	1.00[ASW][hapmap];0.94[CEU][hapmap];0.87[GIH][hapmap];1.00[YRI][hapmap]
rs360798	0.94[CEU][hapmap];0.88[GIH][hapmap]
rs360802	0.89[CEU][hapmap];0.88[GIH][hapmap]
rs6545973	0.89[MKK][hapmap]
rs6545974	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs67657712	0.91[AFR][1000 genomes];0.88[EUR][1000 genomes]

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
rs2539986	VPS54	cis	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:63102400-63146200	Weak transcription	Aorta	Aorta
2	chr2:63102600-63149800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:63102800-63150200	Weak transcription	Esophagus	oesophagus
4	chr2:63104000-63147800	Weak transcription	Fetal Stomach	stomach
5	chr2:63106000-63149600	Weak transcription	Stomach Smooth Muscle	stomach
6	chr2:63106200-63149400	Weak transcription	Ovary	ovary
7	chr2:63106400-63138000	Weak transcription	Fetal Muscle Leg	muscle
8	chr2:63107000-63150200	Weak transcription	HSMM	muscle
9	chr2:63107200-63141600	Weak transcription	Primary B cells from cord blood	blood
10	chr2:63107200-63146000	Weak transcription	Primary hematopoietic stem cells	blood
11	chr2:63107200-63146000	Weak transcription	Left Ventricle	heart
12	chr2:63108200-63149200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr2:63108200-63149600	Weak transcription	Fetal Lung	lung
14	chr2:63119000-63137000	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr2:63122400-63137600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr2:63122800-63166600	Weak transcription	HMEC	breast
17	chr2:63123000-63149400	Weak transcription	NHLF	lung
18	chr2:63123600-63141000	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr2:63123600-63144200	Weak transcription	A549	lung
20	chr2:63123600-63146200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr2:63123600-63148800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr2:63123800-63149800	Weak transcription	NHEK	skin
23	chr2:63126200-63146000	Weak transcription	Primary T cells from cord blood	blood
24	chr2:63127000-63139400	Weak transcription	Adipose Nuclei	Adipose
25	chr2:63129400-63148800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr2:63131200-63137400	Strong transcription	HepG2	liver
27	chr2:63131200-63148600	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr2:63131400-63149800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr2:63131600-63149400	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr2:63131800-63136600	Weak transcription	Fetal Intestine Large	intestine
31	chr2:63131800-63140000	Weak transcription	Fetal Intestine Small	intestine
32	chr2:63131800-63147000	Weak transcription	Liver	Liver
33	chr2:63132000-63139800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr2:63132200-63135400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr2:63132600-63140200	Weak transcription	NHDF-Ad	bronchial
36	chr2:63133600-63149200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr2:63134800-63139800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr2:63134800-63144200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr2:63134800-63147200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr2:63135000-63147000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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