Variant report

Variant	rs12714145
Chromosome Location	chr2:85787341-85787342
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:23)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:85786943-85787358	HepG2	liver:	n/a	n/a
2	HEY1	chr2:85786754-85787395	HepG2	liver:	n/a	n/a
3	TEAD4	chr2:85786684-85787350	HepG2	liver:	n/a	n/a
4	EP300	chr2:85786765-85787342	HepG2	liver:	n/a	n/a
5	POLR2A	chr2:85786767-85789717	HepG2	liver:	n/a	n/a
6	MYBL2	chr2:85786707-85787353	HepG2	liver:	n/a	n/a
7	MYBL2	chr2:85786736-85787493	HepG2	liver:	n/a	n/a
8	HDAC2	chr2:85786826-85787345	HepG2	liver:	n/a	n/a

No data

(count:23 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:85786982..85789648-chr2:85837896..85843296,4	MCF-7	breast:
2	chr2:85644876..85649493-chr2:85786296..85791442,7	MCF-7	breast:
3	chr2:85786998..85790131-chr2:85804287..85808110,8	MCF-7	breast:
4	chr2:85644868..85648304-chr2:85783356..85788933,7	MCF-7	breast:
5	chr2:85635544..85709381-chr2:85757395..85791508,633	K562	blood:
6	chr2:85785429..85790468-chr2:85820934..85826927,9	MCF-7	breast:
7	chr2:85787126..85789513-chr2:85826931..85829549,2	K562	blood:
8	chr2:85786233..85788829-chr2:85802669..85804855,3	K562	blood:
9	chr2:85552687..85556977-chr2:85784981..85789201,5	K562	blood:
10	chr2:85609654..85691056-chr2:85759187..85790499,656	K562	blood:
11	chr2:85784214..85789573-chr2:85827295..85831622,10	MCF-7	breast:
12	chr2:85771408..85781005-chr2:85784986..85791406,15	MCF-7	breast:
13	chr2:85765231..85769518-chr2:85784806..85790228,6	MCF-7	breast:
14	chr2:85539823..85542661-chr2:85786537..85789021,2	K562	blood:
15	chr2:85786233..85790202-chr2:85803177..85805521,3	K562	blood:
16	chr2:85787265..85788881-chr2:85843374..85845144,2	K562	blood:
17	chr2:85786482..85790460-chr2:85816178..85820132,9	MCF-7	breast:
18	chr2:85553459..85556724-chr2:85785432..85789140,4	MCF-7	breast:
19	chr2:85580977..85583407-chr2:85787270..85789639,2	MCF-7	breast:
20	chr2:85785973..85791563-chr2:85836230..85840689,7	MCF-7	breast:
21	chr2:85787036..85790013-chr2:85817133..85820348,4	MCF-7	breast:
22	chr2:85786921..85788482-chr2:85822883..85825336,2	MCF-7	breast:
23	chr2:85634213..85635735-chr2:85786387..85788534,2	MCF-7	breast:

No data

Variant related genes	Relation type
VAMP8	TF binding region
ENSG00000207207	Chromatin interaction
ENSG00000168894	Chromatin interaction
ENSG00000246575	Chromatin interaction
ENSG00000168887	Chromatin interaction
ENSG00000168899	Chromatin interaction
ENSG00000244399	Chromatin interaction
ENSG00000168883	Chromatin interaction
ENSG00000115486	Chromatin interaction
ENSG00000042493	Chromatin interaction
ENSG00000152291	Chromatin interaction
ENSG00000042445	Chromatin interaction
ENSG00000168906	Chromatin interaction
ENSG00000273196	Chromatin interaction
ENSG00000168890	Chromatin interaction
ENSG00000252293	Chromatin interaction
ENSG00000118640	Chromatin interaction
ENSG00000199936	Chromatin interaction
ENSG00000152292	Chromatin interaction
ENSG00000115459	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1010	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1011	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10172544	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10175792	0.93[ASN][1000 genomes]
rs10176176	0.94[ASN][1000 genomes]
rs10179195	0.94[ASN][1000 genomes]
rs10187424	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10198569	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10206961	0.88[ASN][1000 genomes]
rs1058588	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1078004	0.95[ASN][1000 genomes]
rs11891260	0.93[ASN][1000 genomes]
rs12473819	0.95[ASN][1000 genomes]
rs13394343	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1561198	0.91[ASN][1000 genomes]
rs1562323	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17026396	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1972297	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2028900	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2044474	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2366639	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2886722	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35215812	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3731827	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3755014	0.94[ASN][1000 genomes]
rs3755015	0.94[ASN][1000 genomes]
rs3770098	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55971080	0.88[ASN][1000 genomes]
rs59877521	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6547620	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6547621	0.95[ASN][1000 genomes]
rs6547624	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6705839	0.90[ASN][1000 genomes]
rs6705971	0.94[ASN][1000 genomes]
rs6714157	0.93[ASN][1000 genomes]
rs6714709	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6721924	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6731005	0.92[ASN][1000 genomes]
rs6733913	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6735152	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6738645	0.99[ASN][1000 genomes]
rs6739015	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6743030	0.93[ASN][1000 genomes]
rs6750832	0.85[ASN][1000 genomes]
rs6750847	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6757263	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67988001	0.81[ASN][1000 genomes]
rs7568458	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7605975	0.95[ASN][1000 genomes]
rs762684	0.81[ASN][1000 genomes]

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12714145	GGCX	cis	Artery Aorta	GTEx
rs12714145	VAMP8	Cis_1M	lymphoblastoid	RTeQTL
rs12714145	VAMP8	cis	Esophagus Mucosa	GTEx
rs12714145	GGCX	Cis_1M	lymphoblastoid	RTeQTL
rs12714145	GGCX	cis	Whole Blood	GTEx
rs12714145	VAMP8	cis	multi-tissue	Pritchard
rs12714145	GGCX	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85769400-85787800	Weak transcription	Right Atrium	heart
2	chr2:85769800-85788000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:85770200-85787800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:85779600-85787600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr2:85782000-85787800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr2:85782400-85787600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr2:85782400-85787600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr2:85782400-85787600	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr2:85782600-85787600	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr2:85782600-85787800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr2:85782800-85787800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:85782800-85788000	Weak transcription	Aorta	Aorta
13	chr2:85783000-85787800	Weak transcription	Ovary	ovary
14	chr2:85783200-85788200	Weak transcription	Small Intestine	intestine
15	chr2:85785800-85787600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr2:85786000-85787400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
17	chr2:85786200-85787400	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr2:85786200-85787600	Weak transcription	Fetal Intestine Large	intestine
19	chr2:85786200-85787600	Weak transcription	Spleen	Spleen
20	chr2:85786200-85787800	Weak transcription	Esophagus	oesophagus
21	chr2:85786200-85787800	Weak transcription	Fetal Kidney	kidney
22	chr2:85786400-85787400	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr2:85786400-85787600	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr2:85786400-85787600	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr2:85786400-85787600	Weak transcription	Primary hematopoietic stem cells	blood
26	chr2:85786400-85787600	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr2:85786400-85787600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr2:85786400-85787600	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr2:85786400-85787600	Enhancers	Stomach Smooth Muscle	stomach
30	chr2:85786400-85787800	Weak transcription	Thymus	Thymus
31	chr2:85786600-85787600	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr2:85786600-85787600	Weak transcription	Fetal Brain Female	brain
33	chr2:85786800-85787400	Flanking Active TSS	Liver	Liver
34	chr2:85786800-85787600	Enhancers	Adipose Nuclei	Adipose
35	chr2:85786800-85787600	Enhancers	Brain Hippocampus Middle	brain
36	chr2:85786800-85787800	Enhancers	Primary T helper cells fromperipheralblood	blood
37	chr2:85786800-85787800	Enhancers	Fetal Brain Male	brain
38	chr2:85787000-85787400	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr2:85787000-85787400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr2:85787000-85787400	Flanking Active TSS	Hela-S3	cervix
41	chr2:85787000-85787600	Enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr2:85787000-85787600	Enhancers	Cortex derived primary cultured neurospheres	brain
43	chr2:85787000-85787600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr2:85787000-85787600	Enhancers	Brain Germinal Matrix	brain
45	chr2:85787000-85787600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
46	chr2:85787000-85787600	Enhancers	Duodenum Smooth Muscle	Duodenum
47	chr2:85787000-85787600	Enhancers	Fetal Intestine Small	intestine
48	chr2:85787000-85787600	Genic enhancers	Fetal Stomach	stomach
49	chr2:85787000-85787600	Enhancers	HMEC	breast
50	chr2:85787000-85787600	Enhancers	HUVEC	blood vessel

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