Variant report

Variant	rs13406611
Chromosome Location	chr2:85752584-85752585
allele	A/G
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	chr2:85641996..85644852-chr2:85750907..85753427,2	K562	blood:
2	chr2:85744073..85747943-chr2:85749869..85754586,8	K562	blood:
3	chr2:85645966..85650126-chr2:85748875..85752927,8	MCF-7	breast:
4	chr2:85662661..85664817-chr2:85751854..85754599,2	K562	blood:
5	chr2:85752002..85755220-chr2:85755713..85758513,4	K562	blood:
6	chr2:85646542..85649461-chr2:85750442..85753176,2	K562	blood:
7	chr2:85683833..85685364-chr2:85751409..85753280,2	MCF-7	breast:
8	chr2:85622932..85625793-chr2:85749685..85753171,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000042493	Chromatin interaction
ENSG00000152292	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10166612	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10167018	0.96[ASN][1000 genomes]
rs10172793	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10174551	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10179904	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10187218	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10190585	0.96[ASN][1000 genomes]
rs10196357	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10198001	0.87[ASN][1000 genomes]
rs10198761	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10202828	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10496316	0.96[ASN][1000 genomes]
rs12714142	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12714143	1.00[ASN][1000 genomes]
rs12714144	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12714146	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12714147	0.86[ASN][1000 genomes]
rs12994163	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13000511	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13387999	0.86[ASN][1000 genomes]
rs13394092	0.86[ASN][1000 genomes]
rs13406935	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13408713	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13409377	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13421434	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13425821	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13426038	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13429968	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13431159	0.86[ASN][1000 genomes]
rs13431962	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13432584	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17430670	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17508727	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17735885	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2121397	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28398892	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28479378	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28564788	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28800839	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28810460	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34212016	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34214220	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34565621	0.85[AMR][1000 genomes]
rs34669893	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34824628	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35776719	0.85[ASN][1000 genomes]
rs55892665	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56359002	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62165899	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62165905	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62165907	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6727614	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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
rs13406611	VAMP5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:72 , 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	chr2:85749400-85752600	Enhancers	Rectal Mucosa Donor 31	rectum
4	chr2:85750000-85752600	Enhancers	Colonic Mucosa	Colon
5	chr2:85750200-85752600	Enhancers	Lung	lung
6	chr2:85750200-85753000	Enhancers	Fetal Intestine Small	intestine
7	chr2:85750200-85753000	Enhancers	Rectal Mucosa Donor 29	rectum
8	chr2:85750400-85752600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr2:85750400-85752600	Enhancers	Brain Inferior Temporal Lobe	brain
10	chr2:85750400-85752600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
11	chr2:85750400-85752800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr2:85750400-85752800	Enhancers	Brain Anterior Caudate	brain
13	chr2:85750400-85752800	Enhancers	Brain Hippocampus Middle	brain
14	chr2:85750400-85752800	Enhancers	Fetal Intestine Large	intestine
15	chr2:85750400-85752800	Enhancers	Fetal Stomach	stomach
16	chr2:85750400-85752800	Enhancers	Left Ventricle	heart
17	chr2:85750400-85753000	Enhancers	Brain Cingulate Gyrus	brain
18	chr2:85750400-85753000	Enhancers	Duodenum Mucosa	Duodenum
19	chr2:85750400-85753000	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr2:85750400-85754600	Weak transcription	Liver	Liver
21	chr2:85750600-85752600	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr2:85750600-85752600	Enhancers	Fetal Lung	lung
23	chr2:85750600-85752600	Enhancers	Rectal Smooth Muscle	rectum
24	chr2:85750600-85752800	Enhancers	Brain Angular Gyrus	brain
25	chr2:85750600-85752800	Enhancers	Colon Smooth Muscle	Colon
26	chr2:85750600-85752800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr2:85750600-85753200	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr2:85750800-85752600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:85750800-85752600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr2:85750800-85752600	Enhancers	Brain Substantia Nigra	brain
31	chr2:85750800-85752800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr2:85750800-85752800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr2:85750800-85752800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr2:85750800-85752800	Enhancers	Fetal Muscle Trunk	muscle
35	chr2:85750800-85753000	Enhancers	Fetal Muscle Leg	muscle
36	chr2:85750800-85753000	Enhancers	Placenta	Placenta
37	chr2:85750800-85753000	Enhancers	Stomach Mucosa	stomach
38	chr2:85750800-85753000	Enhancers	Hela-S3	cervix
39	chr2:85750800-85753200	Enhancers	Primary neutrophils fromperipheralblood	blood
40	chr2:85751000-85752600	Enhancers	Adipose Nuclei	Adipose
41	chr2:85751000-85752800	Enhancers	Primary hematopoietic stem cells	blood
42	chr2:85751000-85753000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr2:85751000-85753000	Enhancers	Stomach Smooth Muscle	stomach
44	chr2:85751200-85752600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr2:85751200-85753000	Enhancers	Fetal Thymus	thymus
46	chr2:85751200-85764000	Weak transcription	Psoas Muscle	Psoas
47	chr2:85751200-85764400	Weak transcription	Small Intestine	intestine
48	chr2:85751400-85752600	Enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr2:85751400-85753000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr2:85751600-85752600	Enhancers	iPS-15b Cell Line	embryonic stem cell

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