Variant report

Variant	rs13394092
Chromosome Location	chr2:85815954-85815955
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUND	chr2:85815834-85816004	K562	blood:	n/a	n/a
2	NR2F2	chr2:85815666-85816171	K562	blood:	n/a	n/a
3	NR2F2	chr2:85814556-85816546	K562	blood:	n/a	n/a
4	POLR2A	chr2:85815448-85816114	K562	blood:	n/a	n/a
5	EGR1	chr2:85815804-85816075	K562	blood:	n/a	chr2:85815981-85815991 chr2:85815981-85815994
6	POLR2A	chr2:85815759-85816154	K562	blood:	n/a	n/a
7	ZMIZ1	chr2:85815848-85816032	K562	blood:	n/a	n/a
8	YY1	chr2:85815884-85816040	K562	blood:	n/a	n/a
9	TAL1	chr2:85815806-85816192	K562	blood:	n/a	n/a
10	TEAD4	chr2:85815735-85816116	K562	blood:	n/a	n/a
11	EGR1	chr2:85815771-85816162	K562	blood:	n/a	chr2:85815981-85815991 chr2:85815981-85815994
12	EP300	chr2:85815812-85816133	K562	blood:	n/a	n/a
13	RCOR1	chr2:85815779-85816060	K562	blood:	n/a	n/a
14	REST	chr2:85815771-85816069	K562	blood:	n/a	chr2:85815896-85815909
15	GATA2	chr2:85815690-85816185	K562	blood:	n/a	chr2:85815927-85815935
16	POLR2A	chr2:85815724-85816162	K562	blood:	n/a	n/a
17	HDAC2	chr2:85815765-85816063	K562	blood:	n/a	n/a
18	TBL1XR1	chr2:85815945-85815960	K562	blood:	n/a	n/a
19	REST	chr2:85815876-85816057	K562	blood:	n/a	chr2:85815896-85815909
20	GABPA	chr2:85815757-85816140	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:85767675..85769335-chr2:85814210..85816393,2	K562	blood:
2	chr2:85764946..85769175-chr2:85814893..85818821,4	K562	blood:
3	chr2:85786992..85789142-chr2:85815004..85816921,3	MCF-7	breast:
4	chr2:85777404..85779175-chr2:85815499..85818057,2	K562	blood:

Variant related genes	Relation type
VAMP5	TF binding region
ENSG00000168906	Chromatin interaction
ENSG00000118640	Chromatin interaction
ENSG00000115486	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10166612	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10167018	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10172793	0.86[ASN][1000 genomes]
rs10174551	1.00[JPT][hapmap]
rs10179904	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10187218	0.93[ASN][1000 genomes]
rs10190585	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10196357	0.86[ASN][1000 genomes]
rs10198001	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs10198761	0.93[ASN][1000 genomes]
rs10202828	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10496316	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12714142	0.80[ASN][1000 genomes]
rs12714143	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12714144	0.86[ASN][1000 genomes]
rs12714146	0.86[ASN][1000 genomes]
rs12714147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13000511	0.93[ASN][1000 genomes]
rs13387999	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13406611	0.86[ASN][1000 genomes]
rs13406935	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs13408713	0.86[ASN][1000 genomes]
rs13409377	0.93[ASN][1000 genomes]
rs13421434	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs13425821	0.93[ASN][1000 genomes]
rs13426038	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs13429968	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs13431159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13431962	0.86[ASN][1000 genomes]
rs13432584	0.93[ASN][1000 genomes]
rs17430670	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17508727	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17508809	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs17735885	0.86[ASN][1000 genomes]
rs2121397	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs28398892	0.86[ASN][1000 genomes]
rs28479378	0.82[ASN][1000 genomes]
rs28564788	0.89[ASN][1000 genomes]
rs28800839	0.86[ASN][1000 genomes]
rs28810460	0.86[ASN][1000 genomes]
rs34212016	0.93[ASN][1000 genomes]
rs34214220	0.93[ASN][1000 genomes]
rs34669893	0.86[ASN][1000 genomes]
rs34824628	0.86[ASN][1000 genomes]
rs35776719	0.93[ASN][1000 genomes]
rs55892665	0.89[ASN][1000 genomes]
rs56359002	0.93[ASN][1000 genomes]
rs62165899	0.86[ASN][1000 genomes]
rs62165905	0.86[ASN][1000 genomes]
rs62165907	0.89[ASN][1000 genomes]
rs6727614	0.86[ASN][1000 genomes]
rs7569073	0.87[CEU][hapmap];1.00[CHB][hapmap]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13394092	VAMP5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85812000-85816000	Enhancers	Spleen	Spleen
2	chr2:85812400-85816000	Enhancers	Primary B cells from cord blood	blood
3	chr2:85812400-85818600	Enhancers	Placenta	Placenta
4	chr2:85812400-85818600	Enhancers	Lung	lung
5	chr2:85812600-85819200	Enhancers	Fetal Muscle Leg	muscle
6	chr2:85812600-85821200	Weak transcription	Fetal Heart	heart
7	chr2:85812800-85817200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr2:85812800-85817800	Enhancers	NHLF	lung
9	chr2:85812800-85818800	Enhancers	Psoas Muscle	Psoas
10	chr2:85812800-85819000	Enhancers	Primary hematopoietic stem cells	blood
11	chr2:85813000-85816400	Weak transcription	Gastric	stomach
12	chr2:85813000-85817000	Enhancers	HepG2	liver
13	chr2:85813000-85817200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr2:85813000-85817200	Weak transcription	Esophagus	oesophagus
15	chr2:85813000-85817200	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr2:85813000-85817400	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr2:85813000-85818200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr2:85813000-85819600	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr2:85813200-85816000	Weak transcription	Brain Substantia Nigra	brain
20	chr2:85813200-85817000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr2:85813200-85817200	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr2:85813200-85817400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr2:85813200-85817400	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr2:85813200-85817800	Enhancers	Primary neutrophils fromperipheralblood	blood
25	chr2:85813200-85817800	Enhancers	Adipose Nuclei	Adipose
26	chr2:85813200-85821400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr2:85813400-85816200	Enhancers	Skeletal Muscle Male	skeletal muscle
28	chr2:85813400-85816200	Weak transcription	Osteobl	bone
29	chr2:85813400-85816400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr2:85813400-85816400	Weak transcription	NH-A	brain
31	chr2:85813400-85817000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr2:85813400-85817200	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr2:85813400-85817200	Weak transcription	HMEC	breast
34	chr2:85813400-85817200	Weak transcription	NHEK	skin
35	chr2:85813400-85817400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr2:85813400-85817400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr2:85813400-85817400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr2:85813400-85818400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr2:85813400-85819000	Enhancers	Right Atrium	heart
40	chr2:85813600-85821400	Weak transcription	Fetal Intestine Large	intestine
41	chr2:85813800-85820000	Weak transcription	Fetal Intestine Small	intestine
42	chr2:85814000-85816800	Enhancers	K562	blood
43	chr2:85814000-85821600	Weak transcription	Small Intestine	intestine
44	chr2:85814200-85816200	Enhancers	Fetal Thymus	thymus
45	chr2:85814200-85816200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
46	chr2:85814200-85818800	Enhancers	Duodenum Smooth Muscle	Duodenum
47	chr2:85814600-85817800	Enhancers	NHDF-Ad	bronchial
48	chr2:85814600-85819400	Enhancers	Fetal Lung	lung
49	chr2:85814600-85819600	Enhancers	Left Ventricle	heart
50	chr2:85814600-85819600	Enhancers	Skeletal Muscle Female	skeletal muscle

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