Variant report

Variant	rs11891495
Chromosome Location	chr2:85826721-85826722
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:50)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:85825703-85830272	K562	blood:	n/a	n/a
2	POLR2A	chr2:85826246-85826833	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr2:85825162-85830624	HepG2	liver:	n/a	n/a
4	POLR2A	chr2:85825892-85830647	HepG2	liver:	n/a	n/a
5	MBD4	chr2:85826305-85827136	HepG2	liver:	n/a	n/a
6	POLR2A	chr2:85826677-85827668	PANC-1	pancreas:	n/a	n/a
7	POLR2A	chr2:85826321-85826894	GM12891	blood:	n/a	n/a
8	POLR2A	chr2:85826637-85826760	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr2:85826337-85828052	U87	brain:	n/a	n/a
10	POLR2A	chr2:85826211-85827517	K562	blood:	n/a	n/a
11	POLR2A	chr2:85826113-85827512	GM12891	blood:	n/a	n/a
12	POLR2A	chr2:85826219-85830199	HepG2	liver:	n/a	n/a
13	POLR2A	chr2:85826484-85827534	GM12878	blood:	n/a	n/a
14	POLR2A	chr2:85826447-85827575	HL-60	blood:	n/a	n/a
15	POLR2A	chr2:85826598-85826872	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr2:85826476-85827530	PANC-1	pancreas:	n/a	n/a
17	POLR2A	chr2:85826645-85827143	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr2:85826547-85827284	GM19193	blood:	n/a	n/a
19	POLR2A	chr2:85826597-85826974	HepG2	liver:	n/a	n/a
20	POLR2A	chr2:85826549-85827663	Hela-S3	cervix:	n/a	n/a
21	CTCF	chr2:85826640-85826790	HepG2	liver:	n/a	n/a
22	POLR2A	chr2:85825695-85830271	K562	blood:	n/a	n/a
23	POLR2A	chr2:85825646-85827771	K562	blood:	n/a	n/a
24	HEY1	chr2:85825187-85827776	HepG2	liver:	n/a	n/a
25	POLR2A	chr2:85826549-85827524	GM12878	blood:	n/a	n/a
26	POLR2A	chr2:85826569-85827335	A549	lung:	n/a	n/a
27	POLR2A	chr2:85826258-85827333	GM12892	blood:	n/a	n/a
28	HEY1	chr2:85826687-85826876	K562	blood:	n/a	n/a
29	POLR2A	chr2:85826353-85827565	MCF-7	breast:	n/a	n/a
30	POLR2A	chr2:85826650-85826842	A549	lung:	n/a	n/a
31	POLR2A	chr2:85826695-85826969	HUVEC	blood vessel:	n/a	n/a
32	POLR2A	chr2:85825540-85828209	K562	blood:	n/a	n/a
33	POLR2A	chr2:85826545-85827362	GM12891	blood:	n/a	n/a
34	USF2	chr2:85826636-85826722	HepG2	liver:	n/a	n/a
35	POLR2A	chr2:85825877-85830216	GM12878	blood:	n/a	n/a
36	POLR2A	chr2:85826366-85828018	HepG2	liver:	n/a	n/a
37	POLR2A	chr2:85826415-85827531	HUVEC	blood vessel:	n/a	n/a
38	POLR2A	chr2:85825881-85827633	GM12878	blood:	n/a	n/a
39	POLR2A	chr2:85825324-85830119	K562	blood:	n/a	n/a
40	POLR2A	chr2:85826468-85827406	GM12891	blood:	n/a	n/a
41	POLR2A	chr2:85826331-85828576	U87	brain:	n/a	n/a
42	POLR2A	chr2:85825709-85827553	HepG2	liver:	n/a	n/a
43	POLR2A	chr2:85826452-85827625	GM12892	blood:	n/a	n/a
44	POLR2A	chr2:85826664-85827040	HCT-116	colon:	n/a	n/a
45	POLR2A	chr2:85826479-85827549	PFSK-1	brain:	n/a	n/a
46	POLR2A	chr2:85821285-85828013	HepG2	liver:	n/a	n/a
47	POLR2A	chr2:85826638-85826861	MCF-7	breast:	n/a	n/a
48	POLR2A	chr2:85826618-85826990	A549	lung:	n/a	n/a
49	POLR2A	chr2:85826476-85828007	GM12892	blood:	n/a	n/a
50	POLR2A	chr2:85826673-85827124	PBDE	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:85802926..85807956-chr2:85820760..85828546,8	K562	blood:
2	chr2:85764595..85768669-chr2:85824476..85831716,9	MCF-7	breast:
3	chr2:85785429..85790468-chr2:85820934..85826927,9	MCF-7	breast:
4	chr2:85645470..85649377-chr2:85826700..85831557,5	MCF-7	breast:
5	chr2:85764454..85770994-chr2:85819148..85831427,14	K562	blood:
6	chr2:85764018..85768553-chr2:85822883..85829718,12	MCF-7	breast:
7	chr2:85765237..85769549-chr2:85821409..85826975,10	K562	blood:
8	chr2:85782564..85785342-chr2:85825387..85826998,2	MCF-7	breast:

No data

Variant related genes	Relation type
USP39	TF binding region
ENSG00000115486	Chromatin interaction
ENSG00000152292	Chromatin interaction
ENSG00000118640	Chromatin interaction
ENSG00000042493	Chromatin interaction
ENSG00000168906	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12463933	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1374370	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs14976	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17508809	0.89[ASW][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs17508843	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.84[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2289976	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2304566	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34623563	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56192500	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62166770	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62166779	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72843872	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7569073	1.00[ASW][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11891495	VAMP5	Cis_1M	lymphoblastoid	RTeQTL
rs11891495	GGCX	cis	cerebellum	SCAN
rs11891495	VAMP8	Cis_1M	lymphoblastoid	RTeQTL
rs11891495	GGCX	cis	parietal	SCAN
rs11891495	VAMP5	cis	Esophagus Mucosa	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85823200-85829200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:85823600-85829000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:85823800-85828800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr2:85824000-85826800	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr2:85824000-85826800	Strong transcription	Fetal Lung	lung
6	chr2:85824000-85826800	Strong transcription	Left Ventricle	heart
7	chr2:85824000-85827000	Strong transcription	H9 Cell Line	embryonic stem cell
8	chr2:85824000-85827000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr2:85824000-85827600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr2:85824000-85827600	Strong transcription	Aorta	Aorta
11	chr2:85824000-85828200	Genic enhancers	Liver	Liver
12	chr2:85824000-85828400	Genic enhancers	Skeletal Muscle Male	skeletal muscle
13	chr2:85824000-85828600	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr2:85824000-85828600	Genic enhancers	Fetal Intestine Small	intestine
15	chr2:85824000-85828800	Weak transcription	Psoas Muscle	Psoas
16	chr2:85824200-85826800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
17	chr2:85824200-85826800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr2:85824200-85827000	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr2:85824200-85827200	Strong transcription	H1 Cell Line	embryonic stem cell
20	chr2:85824200-85827200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr2:85824200-85827200	Strong transcription	Primary T cells from cord blood	blood
22	chr2:85824200-85827200	Strong transcription	Brain Anterior Caudate	brain
23	chr2:85824200-85827400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr2:85824200-85828200	Strong transcription	Fetal Brain Female	brain
25	chr2:85824200-85828400	Strong transcription	Cortex derived primary cultured neurospheres	brain
26	chr2:85824200-85828400	Weak transcription	Right Atrium	heart
27	chr2:85824200-85828600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr2:85824200-85828600	Genic enhancers	Pancreas	Pancrea
29	chr2:85824400-85826800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr2:85824400-85827000	Strong transcription	Osteobl	bone
31	chr2:85824400-85827200	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr2:85824400-85827200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr2:85824400-85827200	Strong transcription	Muscle Satellite Cultured Cells	--
34	chr2:85824400-85827200	Strong transcription	Brain Hippocampus Middle	brain
35	chr2:85824400-85827200	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr2:85824400-85827200	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr2:85824400-85827400	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr2:85824400-85827400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr2:85824400-85827600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr2:85824400-85827800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr2:85824400-85828200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr2:85824400-85828200	Strong transcription	NHLF	lung
43	chr2:85824400-85828400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr2:85824400-85828400	Strong transcription	Fetal Muscle Leg	muscle
45	chr2:85824400-85828600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr2:85824400-85828600	Weak transcription	HUVEC	blood vessel
47	chr2:85824400-85829000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr2:85824600-85826800	Strong transcription	Placenta	Placenta
49	chr2:85824600-85827000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr2:85824600-85827200	Strong transcription	Adipose Nuclei	Adipose

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