Variant report

Variant	rs12714147
Chromosome Location	chr2:85813834-85813835
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:85813565-85814047	HL-60	blood:	n/a	n/a
2	MAX	chr2:85813795-85814019	NB4	blood:	n/a	n/a
3	POLR2A	chr2:85813719-85813919	K562	blood:	n/a	n/a
4	POLR2A	chr2:85813681-85814037	HL-60	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:85764476..85768967-chr2:85811222..85814196,4	MCF-7	breast:
2	chr2:85764082..85769632-chr2:85809376..85814783,9	K562	blood:
3	chr2:85786758..85788830-chr2:85812863..85814655,2	MCF-7	breast:
4	chr2:85788681..85792834-chr2:85809475..85813834,4	MCF-7	breast:

No data

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

Extended variants
information (count: 52 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs10166612	0.87[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];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];0.90[YRI][hapmap]
rs10179904	0.87[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs10187218	0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs10190585	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10196357	0.80[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs10198001	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs10198761	0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs10202828	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.86[ASN][1000 genomes]
rs10496316	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.89[ASN][1000 genomes]
rs12714142	0.80[ASN][1000 genomes]
rs12714143	0.87[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12714144	0.86[ASN][1000 genomes]
rs12714146	0.86[ASN][1000 genomes]
rs13000511	0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs13387999	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13394092	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]
rs13406611	0.86[ASN][1000 genomes]
rs13406935	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs13408713	0.86[ASN][1000 genomes]
rs13409377	0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs13421434	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs13425821	0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs13426038	0.87[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs13429968	0.87[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs13431159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13431962	0.86[ASN][1000 genomes]
rs13432584	0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs17430670	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs17508727	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs17508809	0.87[CEU][hapmap];1.00[CHB][hapmap];0.83[GIH][hapmap];0.86[MKK][hapmap]
rs17735885	0.86[ASN][1000 genomes]
rs2121397	0.87[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs28398892	0.86[ASN][1000 genomes]
rs28479378	0.82[ASN][1000 genomes]
rs28564788	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs28800839	0.86[ASN][1000 genomes]
rs28810460	0.86[ASN][1000 genomes]
rs34212016	0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs34214220	0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs34669893	0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs34824628	0.86[ASN][1000 genomes]
rs35776719	0.93[ASN][1000 genomes]
rs55892665	0.89[ASN][1000 genomes]
rs56359002	0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs62165899	0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs62165905	0.87[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs62165907	0.87[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6727614	0.86[ASN][1000 genomes]
rs7569073	0.88[CEU][hapmap];1.00[CHB][hapmap];0.83[GIH][hapmap]

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12714147	VAMP5	Cis_1M	lymphoblastoid	RTeQTL
rs12714147	GGCX	cis	parietal	SCAN
rs12714147	GGCX	cis	Nerve Tibial	GTEx
rs12714147	GGCX	cis	cerebellum	SCAN
rs12714147	VAMP5	cis	lymphoblastoid	seeQTL
rs12714147	GGCX	cis	Artery Aorta	GTEx

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85811800-85814000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:85812000-85816000	Enhancers	Spleen	Spleen
3	chr2:85812200-85814000	Enhancers	Small Intestine	intestine
4	chr2:85812400-85815600	Weak transcription	Aorta	Aorta
5	chr2:85812400-85816000	Enhancers	Primary B cells from cord blood	blood
6	chr2:85812400-85818600	Enhancers	Placenta	Placenta
7	chr2:85812400-85818600	Enhancers	Lung	lung
8	chr2:85812600-85814800	Weak transcription	Fetal Kidney	kidney
9	chr2:85812600-85815000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr2:85812600-85815000	Weak transcription	Fetal Stomach	stomach
11	chr2:85812600-85815200	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr2:85812600-85815400	Enhancers	Primary T cells fromperipheralblood	blood
13	chr2:85812600-85815800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr2:85812600-85815800	Weak transcription	Ovary	ovary
15	chr2:85812600-85819200	Enhancers	Fetal Muscle Leg	muscle
16	chr2:85812600-85821200	Weak transcription	Fetal Heart	heart
17	chr2:85812800-85814200	Enhancers	Left Ventricle	heart
18	chr2:85812800-85814800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr2:85812800-85815000	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr2:85812800-85815200	Weak transcription	Thymus	Thymus
21	chr2:85812800-85815400	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr2:85812800-85815600	Weak transcription	Colonic Mucosa	Colon
23	chr2:85812800-85817200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr2:85812800-85817800	Enhancers	NHLF	lung
25	chr2:85812800-85818800	Enhancers	Psoas Muscle	Psoas
26	chr2:85812800-85819000	Enhancers	Primary hematopoietic stem cells	blood
27	chr2:85813000-85814000	Enhancers	Right Ventricle	heart
28	chr2:85813000-85814800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr2:85813000-85814800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr2:85813000-85814800	Enhancers	HUVEC	blood vessel
31	chr2:85813000-85815200	Weak transcription	Fetal Muscle Trunk	muscle
32	chr2:85813000-85815400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr2:85813000-85815800	Weak transcription	Rectal Smooth Muscle	rectum
34	chr2:85813000-85816400	Weak transcription	Gastric	stomach
35	chr2:85813000-85817000	Enhancers	HepG2	liver
36	chr2:85813000-85817200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr2:85813000-85817200	Weak transcription	Esophagus	oesophagus
38	chr2:85813000-85817200	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr2:85813000-85817400	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr2:85813000-85818200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr2:85813000-85819600	Enhancers	Primary monocytes fromperipheralblood	blood
42	chr2:85813200-85814000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr2:85813200-85814200	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr2:85813200-85814400	Weak transcription	Primary B cells from peripheral blood	blood
45	chr2:85813200-85814600	Weak transcription	Primary T cells from cord blood	blood
46	chr2:85813200-85814600	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr2:85813200-85814600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr2:85813200-85814600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr2:85813200-85814600	Weak transcription	Fetal Lung	lung
50	chr2:85813200-85814800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links