Variant report

Variant	rs6738009
Chromosome Location	chr2:85737509-85737510
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:85736760..85739875-chr2:85763760..85768991,6	K562	blood:
2	chr2:85735634..85738595-chr2:85739225..85740777,2	K562	blood:
3	chr2:85734925..85738483-chr2:85772502..85775940,3	MCF-7	breast:
4	chr2:85736886..85739082-chr2:85765100..85766701,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168906	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10175792	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10176176	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10179195	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1078004	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11891260	0.84[AMR][1000 genomes]
rs12473819	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13411109	0.83[ASN][1000 genomes]
rs1561198	0.82[AMR][1000 genomes]
rs2166529	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3755014	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3755015	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55971080	0.83[AMR][1000 genomes]
rs6547621	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6705839	0.81[AMR][1000 genomes]
rs6705971	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6714157	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6731005	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6738645	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6743030	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7568458	0.82[AMR][1000 genomes]
rs7591175	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7605975	0.85[AMR][1000 genomes];0.84[EUR][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6738009	GGCX	cis	Whole Blood	GTEx
rs6738009	GGCX	cis	Artery Tibial	GTEx
rs6738009	VAMP8	Cis_1M	lymphoblastoid	RTeQTL
rs6738009	VAMP8	cis	Esophagus Mucosa	GTEx

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85729800-85738000	Weak transcription	Primary monocytes fromperipheralblood	blood
2	chr2:85730600-85738000	Weak transcription	Spleen	Spleen
3	chr2:85732000-85738600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr2:85732400-85738600	Weak transcription	Pancreas	Pancrea
5	chr2:85732400-85742600	Weak transcription	Fetal Intestine Large	intestine
6	chr2:85732400-85743800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr2:85732400-85744200	Weak transcription	Gastric	stomach
8	chr2:85732600-85737800	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr2:85732600-85738600	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr2:85732800-85738000	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr2:85733000-85738000	Weak transcription	Duodenum Mucosa	Duodenum
12	chr2:85733200-85737800	Weak transcription	Fetal Muscle Leg	muscle
13	chr2:85733200-85738000	Weak transcription	HUVEC	blood vessel
14	chr2:85733200-85738200	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr2:85733200-85738400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr2:85733200-85738600	Weak transcription	Brain Substantia Nigra	brain
17	chr2:85733200-85738600	Weak transcription	Colonic Mucosa	Colon
18	chr2:85733200-85738600	Weak transcription	Lung	lung
19	chr2:85733200-85742200	Weak transcription	Fetal Intestine Small	intestine
20	chr2:85733200-85743800	Weak transcription	Esophagus	oesophagus
21	chr2:85733400-85742200	Weak transcription	Psoas Muscle	Psoas
22	chr2:85733600-85738000	Weak transcription	Adipose Nuclei	Adipose
23	chr2:85733600-85738200	Weak transcription	Small Intestine	intestine
24	chr2:85733600-85750600	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr2:85734400-85738000	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr2:85734400-85738000	Weak transcription	A549	lung
27	chr2:85734600-85737800	Weak transcription	Fetal Muscle Trunk	muscle
28	chr2:85734600-85738000	Weak transcription	Stomach Mucosa	stomach
29	chr2:85734600-85738200	Weak transcription	HSMM	muscle
30	chr2:85734600-85738600	Weak transcription	HSMMtube	muscle
31	chr2:85734600-85740800	Weak transcription	Right Atrium	heart
32	chr2:85734600-85750800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr2:85734600-85762000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr2:85734800-85738200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr2:85734800-85738400	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr2:85734800-85743600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr2:85735000-85738000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr2:85735000-85738000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr2:85735000-85738000	Weak transcription	Hela-S3	cervix
40	chr2:85735000-85738200	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr2:85735000-85738600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr2:85735000-85738600	Weak transcription	NHDF-Ad	bronchial
43	chr2:85735000-85738600	Weak transcription	NHLF	lung
44	chr2:85735200-85738000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr2:85736600-85738800	Weak transcription	Placenta	Placenta

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