Variant report

Variant	rs10172793
Chromosome Location	chr2:85744485-85744486
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:1)
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	chr2:85739058..85741304-chr2:85742843..85744856,2	K562	blood:
2	chr2:85744073..85747943-chr2:85749869..85754586,8	K562	blood:
3	chr2:85739186..85748448-chr2:85762345..85768928,20	MCF-7	breast:
4	chr2:85741968..85744955-chr2:85763802..85767184,3	K562	blood:
5	chr2:85742777..85745374-chr2:85747062..85748764,2	MCF-7	breast:
6	chr2:85731450..85735055-chr2:85743773..85747296,3	K562	blood:
7	chr2:85743677..85746034-chr2:85749461..85751561,2	MCF-7	breast:
8	chr2:85739581..85746336-chr2:85762702..85767789,18	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GGCX-5	chr2:85744316-85744567	NONHSAT072010

No data

Variant related genes	Relation type
ENSG00000168906	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	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10167018	0.96[ASN][1000 genomes]
rs10174551	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10179904	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10187218	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10190585	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10196357	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10198001	0.87[ASN][1000 genomes]
rs10198761	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10202828	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10496316	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12714142	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12714143	0.91[AFR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12714144	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12714146	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12714147	0.86[ASN][1000 genomes]
rs12994163	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13000511	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13387999	0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs13394092	0.86[ASN][1000 genomes]
rs13406611	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13406935	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13408713	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13409377	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13421434	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13425821	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13426038	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13429968	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13431159	0.86[ASN][1000 genomes]
rs13431962	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13432584	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17430670	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17508727	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17735885	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2121397	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28398892	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28479378	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28564788	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28800839	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28810460	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34212016	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34214220	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34565621	0.85[AMR][1000 genomes]
rs34669893	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34824628	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35776719	0.85[ASN][1000 genomes]
rs55892665	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56359002	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62165899	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62165905	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62165907	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6727614	0.92[AMR][1000 genomes];1.00[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
rs10172793	VAMP5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85733600-85750600	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr2:85734600-85750800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr2:85734600-85762000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr2:85742200-85744600	Enhancers	Duodenum Mucosa	Duodenum
5	chr2:85742200-85744600	Enhancers	Fetal Intestine Small	intestine
6	chr2:85742200-85744600	Enhancers	Rectal Mucosa Donor 29	rectum
7	chr2:85742400-85744800	Weak transcription	Psoas Muscle	Psoas
8	chr2:85742600-85745200	Enhancers	Fetal Intestine Large	intestine
9	chr2:85742800-85745200	Enhancers	Rectal Mucosa Donor 31	rectum
10	chr2:85743200-85744600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr2:85743200-85745600	Enhancers	Stomach Mucosa	stomach
12	chr2:85743400-85744600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
13	chr2:85743400-85744600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr2:85743400-85744600	Enhancers	Liver	Liver
15	chr2:85743400-85744600	Flanking Active TSS	A549	lung
16	chr2:85743400-85744800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr2:85743400-85744800	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr2:85743400-85745000	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr2:85743600-85744600	Enhancers	Primary hematopoietic stem cells	blood
20	chr2:85743600-85744600	Enhancers	Colonic Mucosa	Colon
21	chr2:85743600-85744600	Enhancers	Sigmoid Colon	Sigmoid Colon
22	chr2:85743600-85744600	Enhancers	HUVEC	blood vessel
23	chr2:85743800-85744600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr2:85743800-85745000	Enhancers	Esophagus	oesophagus
25	chr2:85744000-85744600	Enhancers	Monocytes-CD14+_RO01746	blood
26	chr2:85744000-85745000	Weak transcription	K562	blood
27	chr2:85744000-85750600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr2:85744200-85744600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr2:85744200-85744600	Enhancers	Gastric	stomach
30	chr2:85744200-85745000	Enhancers	Pancreas	Pancrea
31	chr2:85744200-85745000	Enhancers	Small Intestine	intestine
32	chr2:85744200-85745000	Bivalent Enhancer	HepG2	liver
33	chr2:85744400-85745200	Enhancers	Hela-S3	cervix

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