Variant report

Variant	rs62166770
Chromosome Location	chr2:85834641-85834642
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:22)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:22 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:85834144-85835722	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr2:85834512-85834867	K562	blood:	n/a	n/a
3	POLR2A	chr2:85834088-85834687	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr2:85834503-85834785	HCT-116	colon:	n/a	n/a
5	POLR2A	chr2:85834438-85834904	GM12892	blood:	n/a	n/a
6	POLR2A	chr2:85834146-85834975	PANC-1	pancreas:	n/a	n/a
7	POLR2A	chr2:85834249-85834733	HCT-116	colon:	n/a	n/a
8	POLR2A	chr2:85832564-85835446	HepG2	liver:	n/a	n/a
9	POLR2A	chr2:85834380-85835147	PFSK-1	brain:	n/a	n/a
10	POLR2A	chr2:85834618-85834742	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr2:85834484-85834723	HepG2	liver:	n/a	n/a
12	POLR2A	chr2:85830971-85836753	K562	blood:	n/a	n/a
13	POLR2A	chr2:85834186-85835094	K562	blood:	n/a	n/a
14	POLR2A	chr2:85834376-85835098	GM12878	blood:	n/a	n/a
15	POLR2A	chr2:85834233-85835241	HepG2	liver:	n/a	n/a
16	POLR2A	chr2:85834328-85834787	GM12878	blood:	n/a	n/a
17	HEY1	chr2:85834338-85835169	HepG2	liver:	n/a	n/a
18	POLR2A	chr2:85834290-85834761	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr2:85831284-85835767	HepG2	liver:	n/a	n/a
20	POLR2A	chr2:85834295-85834906	HepG2	liver:	n/a	n/a
21	POLR2A	chr2:85834379-85834780	K562	blood:	n/a	n/a
22	POLR2A	chr2:85834280-85834857	GM12892	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:85786409..85789816-chr2:85832001..85837582,5	MCF-7	breast:
2	chr2:85765201..85768026-chr2:85832043..85835271,3	K562	blood:
3	chr2:85797355..85800096-chr2:85833423..85836013,2	K562	blood:

No data

Variant related genes	Relation type
TMEM150A	TF binding region
USP39	TF binding region
ENSG00000118640	Chromatin interaction
ENSG00000115486	Chromatin interaction
ENSG00000168906	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11891495	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12463933	0.89[ASN][1000 genomes]
rs1374370	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs14976	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17508843	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2289976	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2304566	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34623563	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56192500	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62166779	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72843872	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv874459	chr2:85828014-85939207	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv874460	chr2:85828014-85941074	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs62166770	VAMP5	cis	Esophagus Mucosa	GTEx
rs62166770	VAMP5	Cis_1M	lymphoblastoid	RTeQTL
rs62166770	VAMP8	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85830600-85834800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:85830600-85835800	Enhancers	Fetal Heart	heart
3	chr2:85830600-85836000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:85830800-85835600	Enhancers	Right Atrium	heart
5	chr2:85830800-85838200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr2:85830800-85838200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr2:85830800-85838600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr2:85831200-85834800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr2:85831200-85835800	Weak transcription	Small Intestine	intestine
10	chr2:85831400-85834800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr2:85831400-85836000	Genic enhancers	HSMM	muscle
12	chr2:85831600-85835200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr2:85832000-85834800	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr2:85832000-85834800	Weak transcription	Hela-S3	cervix
15	chr2:85832000-85835200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr2:85832000-85835200	Enhancers	HSMMtube	muscle
17	chr2:85832000-85835400	Weak transcription	Rectal Smooth Muscle	rectum
18	chr2:85832000-85836000	Weak transcription	Esophagus	oesophagus
19	chr2:85832000-85836000	Weak transcription	Ovary	ovary
20	chr2:85832000-85837200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr2:85832000-85837600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr2:85832200-85835000	Enhancers	HUVEC	blood vessel
23	chr2:85832200-85835200	Weak transcription	Colonic Mucosa	Colon
24	chr2:85832200-85836000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr2:85832200-85836400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr2:85832400-85837600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr2:85832600-85835800	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr2:85832600-85835800	Genic enhancers	HepG2	liver
29	chr2:85832600-85836800	Strong transcription	A549	lung
30	chr2:85832600-85837000	Enhancers	Psoas Muscle	Psoas
31	chr2:85832800-85835200	Enhancers	Left Ventricle	heart
32	chr2:85832800-85836600	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr2:85832800-85837200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr2:85832800-85837400	Strong transcription	Primary T cells from cord blood	blood
35	chr2:85832800-85837400	Strong transcription	Fetal Thymus	thymus
36	chr2:85832800-85837600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr2:85833000-85835600	Weak transcription	NHEK	skin
38	chr2:85833000-85837400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr2:85833000-85837800	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr2:85833000-85838200	Weak transcription	HMEC	breast
41	chr2:85833200-85836400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr2:85833200-85837000	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr2:85833200-85837000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr2:85833200-85837000	Strong transcription	Duodenum Mucosa	Duodenum
45	chr2:85833200-85837000	Strong transcription	Thymus	Thymus
46	chr2:85833200-85837200	Strong transcription	Primary B cells from peripheral blood	blood
47	chr2:85833200-85837800	Genic enhancers	Primary neutrophils fromperipheralblood	blood
48	chr2:85833400-85834800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr2:85833400-85835000	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr2:85833400-85835200	Weak transcription	Colon Smooth Muscle	Colon

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