Variant report

Variant	rs2886722
Chromosome Location	chr2:85742297-85742298
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:85739186..85748448-chr2:85762345..85768928,20	MCF-7	breast:
2	chr2:85741540..85743418-chr2:85749217..85750940,2	MCF-7	breast:
3	chr2:85741968..85744955-chr2:85763802..85767184,3	K562	blood:
4	chr2:85731894..85733463-chr2:85739808..85742655,2	K562	blood:
5	chr2:85739581..85746336-chr2:85762702..85767789,18	MCF-7	breast:
6	chr2:85647942..85651306-chr2:85740922..85744191,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168906	Chromatin interaction
ENSG00000152292	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1009	0.89[CEU][hapmap];0.81[CHB][hapmap];0.83[TSI][hapmap]
rs1010	0.89[CEU][hapmap];0.80[CHB][hapmap];0.81[TSI][hapmap]
rs10172544	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10179195	0.86[CEU][hapmap];0.86[CHB][hapmap]
rs10187424	0.92[CEU][hapmap];0.81[CHB][hapmap];0.84[TSI][hapmap]
rs10198569	0.92[CEU][hapmap];0.81[CHB][hapmap];0.84[TSI][hapmap]
rs10206961	0.81[CHB][hapmap]
rs1058588	0.89[CEU][hapmap];0.81[CHB][hapmap];0.81[TSI][hapmap]
rs1078004	0.81[CEU][hapmap];0.81[CHB][hapmap]
rs12714145	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13394343	0.81[EUR][1000 genomes]
rs13411109	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1348818	0.81[CHB][hapmap]
rs1561198	0.81[CHB][hapmap]
rs17026396	0.92[CEU][hapmap];0.86[CHB][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs2028900	0.81[CHB][hapmap]
rs2044474	0.92[CEU][hapmap];0.86[CHB][hapmap];0.83[EUR][1000 genomes]
rs2166529	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs34488525	0.94[ASN][1000 genomes]
rs3755015	0.86[CHB][hapmap]
rs3770098	0.89[CEU][hapmap];0.81[CHB][hapmap]
rs59877521	0.83[EUR][1000 genomes]
rs6547620	0.82[EUR][1000 genomes]
rs6547621	0.81[CHB][hapmap]
rs6705971	0.86[CHB][hapmap]
rs6714709	0.83[EUR][1000 genomes]
rs6721924	0.81[EUR][1000 genomes]
rs6733913	0.83[EUR][1000 genomes]
rs6738514	0.86[ASN][1000 genomes]
rs6738645	0.81[CHB][hapmap]
rs6739015	0.83[EUR][1000 genomes]
rs6750847	0.83[EUR][1000 genomes]
rs6757263	0.89[CEU][hapmap];0.81[CHB][hapmap]
rs7568458	0.85[CEU][hapmap];0.81[CHB][hapmap]
rs7587923	0.88[ASN][1000 genomes]
rs7591175	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9751361	0.94[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:13)

SNP	Gene	Cis/trans	Tissue	Source
rs2886722	VAMP8	Cis_1M	lymphoblastoid	RTeQTL
rs2886722	CD8A	cis	cerebellum	SCAN
rs2886722	MAT2A	cis	cerebellum	SCAN
rs2886722	VAMP8	cis	multi-tissue	Pritchard
rs2886722	VAMP8	cis	lymphoblastoid	seeQTL
rs2886722	VAMP8	cis	parietal	SCAN
rs2886722	VAMP8	cis	uninvolved skin	skin_eQTL
rs2886722	LOC388969	cis	multi-tissue	Pritchard
rs2886722	VAMP8	cis	lesional skin	skin_eQTL
rs2886722	GGCX	cis	cerebellum	SCAN
rs2886722	GGCX	cis	parietal	SCAN
rs2886722	RNF103	cis	parietal	SCAN
rs2886722	MAT2A	cis	multi-tissue	Pritchard

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85732400-85742600	Weak transcription	Fetal Intestine Large	intestine
2	chr2:85732400-85743800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:85732400-85744200	Weak transcription	Gastric	stomach
4	chr2:85733200-85743800	Weak transcription	Esophagus	oesophagus
5	chr2:85733600-85750600	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr2:85734600-85750800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr2:85734600-85762000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr2:85734800-85743600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr2:85738800-85743400	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr2:85738800-85744200	Weak transcription	Small Intestine	intestine
11	chr2:85739000-85742400	Weak transcription	Pancreas	Pancrea
12	chr2:85739000-85743400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr2:85739000-85743400	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr2:85739000-85743400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr2:85739000-85743600	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr2:85739000-85743600	Weak transcription	HUVEC	blood vessel
17	chr2:85739000-85743800	Weak transcription	Placenta	Placenta
18	chr2:85739200-85743400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr2:85741000-85742600	Weak transcription	Stomach Mucosa	stomach
20	chr2:85741000-85742800	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr2:85741000-85743600	Weak transcription	Colonic Mucosa	Colon
22	chr2:85741200-85743400	Enhancers	A549	lung
23	chr2:85742000-85743800	Enhancers	Hela-S3	cervix
24	chr2:85742200-85742400	Enhancers	Psoas Muscle	Psoas
25	chr2:85742200-85742800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr2:85742200-85743800	Enhancers	HepG2	liver
27	chr2:85742200-85744600	Enhancers	Duodenum Mucosa	Duodenum
28	chr2:85742200-85744600	Enhancers	Fetal Intestine Small	intestine
29	chr2:85742200-85744600	Enhancers	Rectal Mucosa Donor 29	rectum

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