Variant report

Variant	rs2166529
Chromosome Location	chr2:85742175-85742176
allele	A/C
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: 48 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1009	0.81[CHB][hapmap]
rs1010	0.80[CHB][hapmap]
rs10175792	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10176176	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10179195	0.95[CEU][hapmap];0.86[CHB][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10187424	0.81[CHB][hapmap]
rs10198569	0.81[CHB][hapmap]
rs10206961	0.81[CHB][hapmap];0.81[AMR][1000 genomes]
rs1058588	0.81[CHB][hapmap]
rs1078004	0.92[CEU][hapmap];0.81[CHB][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11891260	0.90[AMR][1000 genomes]
rs12473819	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13394343	0.83[AMR][1000 genomes]
rs13411109	0.94[ASN][1000 genomes]
rs1348818	0.81[CEU][hapmap];0.81[CHB][hapmap]
rs1561198	0.81[CEU][hapmap];0.81[CHB][hapmap];0.82[GIH][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes]
rs17026396	0.86[CHB][hapmap];0.81[AMR][1000 genomes]
rs2028900	0.92[CEU][hapmap];0.81[CHB][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs2044474	0.86[CHB][hapmap];0.81[AMR][1000 genomes]
rs2886722	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]
rs3755014	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3755015	0.92[CEU][hapmap];0.86[CHB][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3770098	0.81[CHB][hapmap]
rs55971080	0.89[AMR][1000 genomes]
rs59877521	0.81[AMR][1000 genomes]
rs6547620	0.81[AMR][1000 genomes]
rs6547621	0.92[CEU][hapmap];0.81[CHB][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6705839	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6705971	0.92[CEU][hapmap];0.86[CHB][hapmap];0.80[GIH][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6714157	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6714709	0.81[AMR][1000 genomes]
rs6731005	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6733913	0.81[AMR][1000 genomes]
rs6738009	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6738514	0.86[ASN][1000 genomes]
rs6738645	0.92[CEU][hapmap];0.81[CHB][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6739015	0.81[AMR][1000 genomes]
rs6743030	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6757263	0.81[CHB][hapmap]
rs7568458	0.85[CEU][hapmap];0.81[CHB][hapmap];0.86[AMR][1000 genomes]
rs7587923	0.88[ASN][1000 genomes]
rs7591175	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7605975	0.93[AMR][1000 genomes];0.87[EUR][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:14)

SNP	Gene	Cis/trans	Tissue	Source
rs2166529	MAT2A	cis	cerebellum	SCAN
rs2166529	VAMP8	cis	multi-tissue	Pritchard
rs2166529	GGCX	cis	cerebellum	SCAN
rs2166529	GGCX	cis	parietal	SCAN
rs2166529	RNF103	cis	parietal	SCAN
rs2166529	VAMP8	cis	lymphoblastoid	seeQTL
rs2166529	GGCX	cis	Artery Tibial	GTEx
rs2166529	VAMP8	cis	uninvolved skin	skin_eQTL
rs2166529	VAMP8	cis	Esophagus Mucosa	GTEx
rs2166529	VAMP8	cis	lesional skin	skin_eQTL
rs2166529	VAMP8	Cis_1M	lymphoblastoid	RTeQTL
rs2166529	VAMP8	cis	parietal	SCAN
rs2166529	RETSAT	cis	cerebellum	SCAN
rs2166529	GGCX	cis	Whole Blood	GTEx

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	chr2:85733200-85742200	Weak transcription	Fetal Intestine Small	intestine
5	chr2:85733200-85743800	Weak transcription	Esophagus	oesophagus
6	chr2:85733400-85742200	Weak transcription	Psoas Muscle	Psoas
7	chr2:85733600-85750600	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr2:85734600-85750800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr2:85734600-85762000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr2:85734800-85743600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr2:85738800-85742200	Weak transcription	HepG2	liver
12	chr2:85738800-85743400	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr2:85738800-85744200	Weak transcription	Small Intestine	intestine
14	chr2:85739000-85742200	Weak transcription	Duodenum Mucosa	Duodenum
15	chr2:85739000-85742200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr2:85739000-85742400	Weak transcription	Pancreas	Pancrea
17	chr2:85739000-85743400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr2:85739000-85743400	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr2:85739000-85743400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr2:85739000-85743600	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr2:85739000-85743600	Weak transcription	HUVEC	blood vessel
22	chr2:85739000-85743800	Weak transcription	Placenta	Placenta
23	chr2:85739200-85743400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr2:85739600-85742200	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr2:85741000-85742600	Weak transcription	Stomach Mucosa	stomach
26	chr2:85741000-85742800	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr2:85741000-85743600	Weak transcription	Colonic Mucosa	Colon
28	chr2:85741200-85743400	Enhancers	A549	lung
29	chr2:85742000-85743800	Enhancers	Hela-S3	cervix

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