Variant report

Variant	rs10202828
Chromosome Location	chr2:85762675-85762676
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:85762359-85762843	GM12892	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:85644216..85654950-chr2:85758513..85769717,70	MCF-7	breast:
2	chr2:85663253..85664901-chr2:85761571..85763604,2	MCF-7	breast:
3	chr2:85579256..85583791-chr2:85762380..85768080,8	MCF-7	breast:
4	chr2:85637558..85640126-chr2:85762094..85764300,2	MCF-7	breast:
5	chr2:85702779..85705594-chr2:85762118..85763957,2	K562	blood:
6	chr2:85635544..85709381-chr2:85757395..85791508,633	K562	blood:
7	chr2:85609654..85691056-chr2:85759187..85790499,656	K562	blood:
8	chr2:85627012..85628603-chr2:85761794..85764774,2	MCF-7	breast:
9	chr2:85642633..85666582-chr2:85757429..85771032,137	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MAT2A-1	chr2:85761648-85763303	NONHSAT072012

No data

Variant related genes	Relation type
RN7SL830P	TF binding region
MAT2A	TF binding region
ENSG00000244399	Chromatin interaction
ENSG00000252293	Chromatin interaction
ENSG00000273196	Chromatin interaction
ENSG00000152292	Chromatin interaction
ENSG00000042445	Chromatin interaction
ENSG00000207207	Chromatin interaction
ENSG00000042493	Chromatin interaction
ENSG00000115459	Chromatin interaction
ENSG00000199936	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10166612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10167018	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10172793	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10174551	0.83[CEU][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10179904	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10187218	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10190585	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10196357	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10198001	0.83[CEU][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10198761	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10496316	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12714142	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12714143	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12714144	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12714146	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12714147	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.86[ASN][1000 genomes]
rs12994163	0.83[CEU][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13000511	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13387999	0.86[ASN][1000 genomes]
rs13394092	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs13406611	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13406935	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13408713	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13409377	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13421434	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13425821	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13426038	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13429968	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13431159	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs13431962	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13432584	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17430670	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17508727	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17508809	1.00[CHB][hapmap]
rs17735885	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2121397	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28398892	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28479378	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28564788	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28800839	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28810460	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34212016	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34214220	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34565621	0.85[AMR][1000 genomes]
rs34669893	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34824628	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35776719	0.85[ASN][1000 genomes]
rs55892665	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56359002	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62165899	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62165905	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62165907	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6727614	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7569073	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10202828	VAMP5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85745000-85764800	Weak transcription	Esophagus	oesophagus
2	chr2:85751200-85764000	Weak transcription	Psoas Muscle	Psoas
3	chr2:85751200-85764400	Weak transcription	Small Intestine	intestine
4	chr2:85752000-85764800	Weak transcription	Gastric	stomach
5	chr2:85752400-85764800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:85752600-85763600	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr2:85753000-85764000	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr2:85758200-85764800	Enhancers	Primary neutrophils fromperipheralblood	blood
9	chr2:85758600-85764200	Weak transcription	Duodenum Mucosa	Duodenum
10	chr2:85758800-85763400	Weak transcription	Pancreas	Pancrea
11	chr2:85759200-85764000	Weak transcription	Liver	Liver
12	chr2:85760000-85762800	Enhancers	K562	blood
13	chr2:85760800-85764000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr2:85761200-85764400	Enhancers	Stomach Mucosa	stomach
15	chr2:85761400-85763000	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr2:85761400-85763000	Enhancers	Brain Substantia Nigra	brain
17	chr2:85761400-85763200	Enhancers	Monocytes-CD14+_RO01746	blood
18	chr2:85761400-85764400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr2:85761400-85764600	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr2:85761400-85764600	Enhancers	Primary hematopoietic stem cells	blood
21	chr2:85761600-85763000	Enhancers	Brain Cingulate Gyrus	brain
22	chr2:85761600-85764600	Enhancers	Fetal Intestine Small	intestine
23	chr2:85761800-85762800	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr2:85761800-85763400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr2:85761800-85763600	Weak transcription	Fetal Intestine Large	intestine
26	chr2:85761800-85763600	Weak transcription	Rectal Smooth Muscle	rectum
27	chr2:85761800-85763600	Weak transcription	NHEK	skin
28	chr2:85761800-85764000	Weak transcription	GM12878-XiMat	blood
29	chr2:85762000-85762800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr2:85762000-85763000	Enhancers	Brain Angular Gyrus	brain
31	chr2:85762000-85764200	Enhancers	Brain Anterior Caudate	brain
32	chr2:85762000-85764200	Enhancers	A549	lung
33	chr2:85762000-85764400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr2:85762200-85763600	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr2:85762200-85763800	Weak transcription	Brain Hippocampus Middle	brain
36	chr2:85762400-85764200	Enhancers	Hela-S3	cervix
37	chr2:85762600-85762800	Enhancers	iPS-20b Cell Line	embryonic stem cell
38	chr2:85762600-85762800	Enhancers	Dnd41	blood
39	chr2:85762600-85763600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr2:85762600-85764200	Weak transcription	Primary B cells from cord blood	blood
41	chr2:85762600-85764200	Enhancers	NHDF-Ad	bronchial

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