Variant report

Variant	rs6705798
Chromosome Location	chr2:63259881-63259882
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	chr2:63258531..63260171-chr2:63276165..63278833,2	K562	blood:
2	chr2:63258531..63260171-chr2:63275245..63278833,3	K562	blood:

Variant related genes	Relation type
ENSG00000115507	Chromatin interaction
ENSG00000231609	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1022110	0.80[EUR][1000 genomes]
rs11682530	0.92[CEU][hapmap];0.90[GIH][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs11893131	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs13389366	0.83[CHB][hapmap]
rs13410889	0.83[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap]
rs1420018	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs1468748	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17027429	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs1850985	0.82[CHB][hapmap]
rs1877026	0.83[CHB][hapmap];0.82[CHD][hapmap]
rs2058566	0.96[CEU][hapmap];0.90[GIH][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs2058567	0.83[EUR][1000 genomes]
rs2075375	0.95[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs2080227	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2215870	0.88[CEU][hapmap];0.90[GIH][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs2421816	0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs2421860	0.83[CHB][hapmap]
rs2430388	0.88[CEU][hapmap];0.90[GIH][hapmap];0.85[TSI][hapmap]
rs2539978	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs2539980	0.92[CEU][hapmap];0.84[GIH][hapmap]
rs2539985	0.85[EUR][1000 genomes]
rs2539987	0.87[CEU][hapmap];0.90[GIH][hapmap];0.82[TSI][hapmap]
rs2710637	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]
rs2710639	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs2710640	0.82[EUR][1000 genomes]
rs2710642	0.96[CEU][hapmap];0.94[GIH][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs2710644	0.83[EUR][1000 genomes]
rs2710648	0.85[MKK][hapmap]
rs6545971	0.90[CEU][hapmap]
rs6545972	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs6545973	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs6714241	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs6739804	0.92[CEU][hapmap];0.90[GIH][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs7557501	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs7567923	0.92[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs7571916	0.81[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	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
4	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
5	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
6	nsv1004678	chr2:63230722-63562484	Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6705798	VPS54	cis	cerebellum	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:63151400-63272200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr2:63209400-63260000	Weak transcription	Aorta	Aorta
3	chr2:63219200-63269800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr2:63219400-63261600	Weak transcription	Brain Angular Gyrus	brain
5	chr2:63224600-63271800	Weak transcription	Esophagus	oesophagus
6	chr2:63224600-63272000	Weak transcription	NHLF	lung
7	chr2:63228000-63267600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr2:63238200-63262800	Weak transcription	Fetal Brain Male	brain
9	chr2:63238400-63267600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr2:63240800-63271800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr2:63240800-63272200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr2:63241200-63261600	Weak transcription	Brain Anterior Caudate	brain
13	chr2:63241400-63261600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr2:63241400-63261600	Weak transcription	NH-A	brain
15	chr2:63244000-63274400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr2:63244200-63274600	Weak transcription	Pancreas	Pancrea
17	chr2:63244400-63260200	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr2:63244600-63261600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr2:63245400-63261600	Weak transcription	Brain Germinal Matrix	brain
20	chr2:63248800-63269400	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr2:63248800-63271600	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr2:63250200-63260800	Weak transcription	Fetal Brain Female	brain
23	chr2:63250200-63262000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr2:63250800-63260800	Weak transcription	Fetal Muscle Leg	muscle
25	chr2:63252600-63271600	Weak transcription	Fetal Stomach	stomach
26	chr2:63255000-63271800	Weak transcription	Colon Smooth Muscle	Colon
27	chr2:63255400-63272600	Weak transcription	Stomach Smooth Muscle	stomach
28	chr2:63255600-63261400	Weak transcription	NHEK	skin
29	chr2:63255600-63272000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr2:63255800-63265400	Weak transcription	Left Ventricle	heart
31	chr2:63255800-63265600	Weak transcription	Adipose Nuclei	Adipose
32	chr2:63256000-63270400	Weak transcription	Primary B cells from cord blood	blood
33	chr2:63256600-63261600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr2:63256600-63262000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr2:63256800-63261400	Weak transcription	HUVEC	blood vessel
36	chr2:63256800-63261600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr2:63256800-63261600	Weak transcription	A549	lung
38	chr2:63256800-63261800	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr2:63256800-63264600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr2:63256800-63265800	Weak transcription	HSMM	muscle
41	chr2:63256800-63265800	Weak transcription	NHDF-Ad	bronchial
42	chr2:63256800-63271800	Weak transcription	Ovary	ovary
43	chr2:63256800-63272200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr2:63256800-63272400	Weak transcription	Osteobl	bone
45	chr2:63256800-63275600	Weak transcription	HMEC	breast
46	chr2:63257000-63267600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr2:63257400-63264600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr2:63257600-63264800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr2:63258800-63261400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr2:63259000-63264600	Weak transcription	Liver	Liver

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