Variant report

Variant	rs6727614
Chromosome Location	chr2:85750853-85750854
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:85744073..85747943-chr2:85749869..85754586,8	K562	blood:
2	chr2:85741540..85743418-chr2:85749217..85750940,2	MCF-7	breast:
3	chr2:85645966..85650126-chr2:85748875..85752927,8	MCF-7	breast:
4	chr2:85646542..85649461-chr2:85750442..85753176,2	K562	blood:
5	chr2:85743677..85746034-chr2:85749461..85751561,2	MCF-7	breast:
6	chr2:85747114..85750093-chr2:85750292..85751803,2	K562	blood:
7	chr2:85622932..85625793-chr2:85749685..85753171,3	MCF-7	breast:
8	chr2:85663235..85666181-chr2:85750315..85752072,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000152292	Chromatin interaction
ENSG00000042493	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10166612	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10167018	0.96[ASN][1000 genomes]
rs10172793	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10174551	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10179904	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10187218	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10190585	0.90[AFR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10196357	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10198001	0.87[ASN][1000 genomes]
rs10198761	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10202828	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10496316	0.90[AFR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12714142	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12714143	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12714144	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12714146	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12714147	0.86[ASN][1000 genomes]
rs12994163	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13000511	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13387999	0.86[ASN][1000 genomes]
rs13394092	0.86[ASN][1000 genomes]
rs13406611	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13406935	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13408713	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13409377	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13421434	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13425821	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13426038	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13429968	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13431159	0.86[ASN][1000 genomes]
rs13431962	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13432584	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17430670	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17508727	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17735885	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2121397	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28398892	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28479378	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28564788	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28800839	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28810460	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34212016	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34214220	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34669893	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34824628	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35776719	0.85[ASN][1000 genomes]
rs55892665	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56359002	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62165899	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62165905	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62165907	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005351	chr2:85242657-85774909	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	198 gene(s)	inside rSNPs	diseases
2	nsv535803	chr2:85242657-85774909	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	198 gene(s)	inside rSNPs	diseases
3	nsv834283	chr2:85609500-85755708	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6727614	VAMP5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85734600-85762000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr2:85745000-85764800	Weak transcription	Esophagus	oesophagus
3	chr2:85748400-85751000	Weak transcription	Psoas Muscle	Psoas
4	chr2:85748600-85751000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr2:85748800-85751800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr2:85749000-85751000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr2:85749400-85752600	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr2:85750000-85752600	Enhancers	Colonic Mucosa	Colon
9	chr2:85750200-85751000	Enhancers	Pancreas	Pancrea
10	chr2:85750200-85751200	Enhancers	Sigmoid Colon	Sigmoid Colon
11	chr2:85750200-85751800	Bivalent Enhancer	HepG2	liver
12	chr2:85750200-85751800	Enhancers	K562	blood
13	chr2:85750200-85752400	Enhancers	A549	lung
14	chr2:85750200-85752600	Enhancers	Lung	lung
15	chr2:85750200-85753000	Enhancers	Fetal Intestine Small	intestine
16	chr2:85750200-85753000	Enhancers	Rectal Mucosa Donor 29	rectum
17	chr2:85750400-85752000	Enhancers	Gastric	stomach
18	chr2:85750400-85752600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr2:85750400-85752600	Enhancers	Brain Inferior Temporal Lobe	brain
20	chr2:85750400-85752600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
21	chr2:85750400-85752800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr2:85750400-85752800	Enhancers	Brain Anterior Caudate	brain
23	chr2:85750400-85752800	Enhancers	Brain Hippocampus Middle	brain
24	chr2:85750400-85752800	Enhancers	Fetal Intestine Large	intestine
25	chr2:85750400-85752800	Enhancers	Fetal Stomach	stomach
26	chr2:85750400-85752800	Enhancers	Left Ventricle	heart
27	chr2:85750400-85753000	Enhancers	Brain Cingulate Gyrus	brain
28	chr2:85750400-85753000	Enhancers	Duodenum Mucosa	Duodenum
29	chr2:85750400-85753000	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr2:85750400-85754600	Weak transcription	Liver	Liver
31	chr2:85750600-85751000	Flanking Active TSS	Stomach Smooth Muscle	stomach
32	chr2:85750600-85751200	Enhancers	Small Intestine	intestine
33	chr2:85750600-85751600	Enhancers	NHDF-Ad	bronchial
34	chr2:85750600-85751800	Enhancers	Fetal Kidney	kidney
35	chr2:85750600-85752000	Enhancers	Right Ventricle	heart
36	chr2:85750600-85752400	Enhancers	Duodenum Smooth Muscle	Duodenum
37	chr2:85750600-85752600	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr2:85750600-85752600	Enhancers	Fetal Lung	lung
39	chr2:85750600-85752600	Enhancers	Rectal Smooth Muscle	rectum
40	chr2:85750600-85752800	Enhancers	Brain Angular Gyrus	brain
41	chr2:85750600-85752800	Enhancers	Colon Smooth Muscle	Colon
42	chr2:85750600-85752800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr2:85750600-85753200	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr2:85750800-85751000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr2:85750800-85751400	Enhancers	Monocytes-CD14+_RO01746	blood
46	chr2:85750800-85751600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr2:85750800-85751800	Enhancers	Primary hematopoietic stem cells short term culture	blood
48	chr2:85750800-85752000	Enhancers	Right Atrium	heart
49	chr2:85750800-85752400	Enhancers	Fetal Heart	heart
50	chr2:85750800-85752400	Enhancers	NHLF	lung

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