Variant report

Variant	rs10172544
Chromosome Location	chr2:85788270-85788271
allele	A/C
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	RELA	chr2:85788244-85788986	GM15510	blood:	n/a	n/a
2	POLR2A	chr2:85788201-85789026	GM12878	blood:	n/a	n/a
3	POLR2A	chr2:85788225-85789139	ProgFib	skin:	n/a	n/a
4	SIN3AK20	chr2:85788028-85788384	H1-hESC	embryonic stem cell:	n/a	n/a
5	GATA3	chr2:85788231-85789402	A549	lung:	n/a	n/a
6	EGR1	chr2:85788000-85788942	K562	blood:	n/a	chr2:85788136-85788149 chr2:85788440-85788450 chr2:85788440-85788453 chr2:85788138-85788148 chr2:85788135-85788150 chr2:85788439-85788453 chr2:85788136-85788150 chr2:85788486-85788496 chr2:85788440-85788453 chr2:85788132-85788154 chr2:85788405-85788415 chr2:85788136-85788149 chr2:85788440-85788453 chr2:85788439-85788454 chr2:85788139-85788148 chr2:85788136-85788149 chr2:85788136-85788149 chr2:85788440-85788453 chr2:85788441-85788450
7	EGR1	chr2:85788050-85789159	HCT-116	colon:	n/a	chr2:85788136-85788149 chr2:85788440-85788450 chr2:85788440-85788453 chr2:85788138-85788148 chr2:85788135-85788150 chr2:85788439-85788453 chr2:85788136-85788150 chr2:85788486-85788496 chr2:85788440-85788453 chr2:85788132-85788154 chr2:85788405-85788415 chr2:85788136-85788149 chr2:85788440-85788453 chr2:85788439-85788454 chr2:85788139-85788148 chr2:85788136-85788149 chr2:85788136-85788149 chr2:85788440-85788453 chr2:85788441-85788450
8	POLR2A	chr2:85788259-85789169	H1-hESC	embryonic stem cell:	n/a	n/a
9	REST	chr2:85787879-85789264	H1-neurons	neurons:	n/a	n/a
10	YY1	chr2:85788233-85788403	K562	blood:	n/a	n/a
11	POLR2A	chr2:85788232-85789160	GM12892	blood:	n/a	n/a
12	YY1	chr2:85788142-85789106	GM12878	blood:	n/a	chr2:85788727-85788738 chr2:85788442-85788451 chr2:85788442-85788453 chr2:85788704-85788713 chr2:85788406-85788415
13	TAF1	chr2:85788110-85789245	H1-hESC	embryonic stem cell:	n/a	n/a
14	CREB1	chr2:85787733-85789314	HepG2	liver:	n/a	n/a
15	RUNX3	chr2:85788002-85789357	GM12878	blood:	n/a	n/a
16	TAF1	chr2:85788154-85789163	ECC-1	luminal epithelium:	n/a	n/a
17	SIN3A	chr2:85788121-85789210	H1-hESC	embryonic stem cell:	n/a	chr2:85788727-85788738
18	MAX	chr2:85788250-85789056	NB4	blood:	n/a	chr2:85788404-85788414 chr2:85788407-85788417 chr2:85788727-85788737
19	TAF1	chr2:85788234-85789203	ECC-1	luminal epithelium:	n/a	n/a
20	CEBPB	chr2:85788178-85788813	Hela-S3	cervix:	n/a	n/a
21	TAF1	chr2:85788106-85789090	H1-neurons	neurons:	n/a	n/a
22	ZBTB7A	chr2:85788136-85789087	K562	blood:	n/a	n/a
23	CHD1	chr2:85788123-85788319	GM12878	blood:	n/a	n/a
24	POLR2A	chr2:85788167-85789407	MCF-7	breast:	n/a	n/a
25	POLR2A	chr2:85788191-85789345	MCF-7	breast:	n/a	n/a
26	POLR2A	chr2:85788248-85789320	PFSK-1	brain:	n/a	n/a
27	YY1	chr2:85788102-85789255	K562	blood:	n/a	chr2:85788727-85788738 chr2:85788442-85788451 chr2:85788442-85788453 chr2:85788704-85788713 chr2:85788406-85788415
28	TBP	chr2:85788249-85789161	H1-hESC	embryonic stem cell:	n/a	n/a
29	MXI1	chr2:85788260-85789162	HepG2	liver:	n/a	n/a
30	RAD21	chr2:85788132-85789101	IMR90	lung:	n/a	chr2:85788730-85788740
31	POLR2A	chr2:85786767-85789717	HepG2	liver:	n/a	n/a
32	YY1	chr2:85788250-85789162	HepG2	liver:	n/a	chr2:85788727-85788738 chr2:85788442-85788451 chr2:85788442-85788453 chr2:85788704-85788713 chr2:85788406-85788415
33	POLR2A	chr2:85788229-85789373	GM12878	blood:	n/a	n/a
34	CREB1	chr2:85788263-85789212	GM12878	blood:	n/a	n/a
35	HEY1	chr2:85788124-85789464	HepG2	liver:	n/a	n/a
36	TBL1XR1	chr2:85788108-85788274	K562	blood:	n/a	n/a
37	POLR2A	chr2:85788224-85789133	MCF-7	breast:	n/a	n/a
38	MAX	chr2:85788205-85789088	K562	blood:	n/a	chr2:85788404-85788414 chr2:85788407-85788417 chr2:85788727-85788737
39	ELF1	chr2:85788092-85789090	GM12878	blood:	n/a	chr2:85788438-85788450 chr2:85788484-85788496
40	POLR2A	chr2:85788125-85789038	H1-neurons	neurons:	n/a	n/a
41	MXI1	chr2:85787838-85789269	IMR90	lung:	n/a	n/a
42	PML	chr2:85788208-85789194	GM12878	blood:	n/a	n/a
43	POLR2A	chr2:85788117-85789114	Hela-S3	cervix:	n/a	n/a
44	RCOR1	chr2:85787954-85789202	K562	blood:	n/a	n/a
45	TAF1	chr2:85788229-85789099	HepG2	liver:	n/a	n/a
46	POLR2A	chr2:85788084-85789304	PFSK-1	brain:	n/a	n/a
47	MAX	chr2:85788071-85789044	GM12878	blood:	n/a	chr2:85788404-85788414 chr2:85788407-85788417 chr2:85788727-85788737
48	SIN3AK20	chr2:85788164-85789246	MCF-7	breast:	n/a	n/a
49	SMARCB1	chr2:85788193-85789092	Hela-S3	cervix:	n/a	n/a
50	TCF12	chr2:85788221-85789198	ECC-1	luminal epithelium:	n/a	n/a

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	chr2:85636488..85639365-chr2:85787637..85789884,2	MCF-7	breast:
5	chr2:85788038..85789914-chr2:85841678..85843321,2	MCF-7	breast:
6	chr2:85644868..85648304-chr2:85783356..85788933,7	MCF-7	breast:
7	chr2:85635544..85709381-chr2:85757395..85791508,633	K562	blood:
8	chr2:85541060..85543065-chr2:85787945..85789826,2	MCF-7	breast:
9	chr2:85785429..85790468-chr2:85820934..85826927,9	MCF-7	breast:
10	chr2:85788151..85788948-chr2:85838607..85839408,2	Hela-S3	cervix:
11	chr2:85787126..85789513-chr2:85826931..85829549,2	K562	blood:
12	chr2:85786233..85788829-chr2:85802669..85804855,3	K562	blood:
13	chr2:85552687..85556977-chr2:85784981..85789201,5	K562	blood:
14	chr2:85609654..85691056-chr2:85759187..85790499,656	K562	blood:
15	chr2:85784214..85789573-chr2:85827295..85831622,10	MCF-7	breast:
16	chr2:85771408..85781005-chr2:85784986..85791406,15	MCF-7	breast:
17	chr2:85765231..85769518-chr2:85784806..85790228,6	MCF-7	breast:
18	chr2:85539823..85542661-chr2:85786537..85789021,2	K562	blood:
19	chr2:85788196..85788770-chr2:85829502..85830256,2	MCF-7	breast:
20	chr2:85786233..85790202-chr2:85803177..85805521,3	K562	blood:
21	chr2:85787265..85788881-chr2:85843374..85845144,2	K562	blood:
22	chr2:85786482..85790460-chr2:85816178..85820132,9	MCF-7	breast:
23	chr2:85553459..85556724-chr2:85785432..85789140,4	MCF-7	breast:
24	chr2:85580977..85583407-chr2:85787270..85789639,2	MCF-7	breast:
25	chr2:85785973..85791563-chr2:85836230..85840689,7	MCF-7	breast:
26	chr2:85787036..85790013-chr2:85817133..85820348,4	MCF-7	breast:
27	chr2:85568800..85571035-chr2:85787413..85790410,2	MCF-7	breast:
28	chr2:85786921..85788482-chr2:85822883..85825336,2	MCF-7	breast:
29	chr2:85787502..85790371-chr2:85804560..85808548,6	MCF-7	breast:
30	chr2:85634213..85635735-chr2:85786387..85788534,2	MCF-7	breast:

Variant related genes	Relation type
VAMP8	TF binding region
ENSG00000270532	Chromatin interaction
ENSG00000115486	Chromatin interaction
ENSG00000168887	Chromatin interaction
ENSG00000168894	Chromatin interaction
ENSG00000168890	Chromatin interaction
ENSG00000118640	Chromatin interaction
ENSG00000199936	Chromatin interaction
ENSG00000152291	Chromatin interaction
ENSG00000042445	Chromatin interaction
ENSG00000246575	Chromatin interaction
ENSG00000207207	Chromatin interaction
ENSG00000168906	Chromatin interaction
ENSG00000168883	Chromatin interaction
ENSG00000244399	Chromatin interaction
ENSG00000168899	Chromatin interaction
ENSG00000115459	Chromatin interaction
ENSG00000252293	Chromatin interaction
ENSG00000042493	Chromatin interaction
ENSG00000152292	Chromatin interaction
ENSG00000273196	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]
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]
rs12714145	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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
rs10172544	VAMP8	Cis_1M	lymphoblastoid	RTeQTL
rs10172544	GGCX	Cis_1M	lymphoblastoid	RTeQTL
rs10172544	VAMP8	cis	multi-tissue	Pritchard
rs10172544	VAMP8	cis	Esophagus Mucosa	GTEx
rs10172544	GGCX	cis	Artery Tibial	GTEx
rs10172544	GGCX	cis	Whole Blood	GTEx
rs10172544	GGCX	cis	Artery Aorta	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85787000-85789400	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr2:85787200-85789400	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr2:85787200-85789400	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr2:85787200-85789400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr2:85787400-85789000	Active TSS	Colonic Mucosa	Colon
6	chr2:85787400-85789200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr2:85787400-85789200	Active TSS	Pancreas	Pancrea
8	chr2:85787400-85789200	Bivalent/Poised TSS	HepG2	liver
9	chr2:85787400-85789400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr2:85787400-85789400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr2:85787400-85789400	Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr2:85787400-85789400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr2:85787400-85789400	Active TSS	A549	lung
14	chr2:85787400-85789400	Active TSS	HSMM	muscle
15	chr2:85787400-85789400	Active TSS	NHLF	lung
16	chr2:85787600-85788400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr2:85787600-85788400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr2:85787600-85788400	Flanking Active TSS	Adipose Nuclei	Adipose
19	chr2:85787600-85789200	Active TSS	H1 Cell Line	embryonic stem cell
20	chr2:85787600-85789200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr2:85787600-85789200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr2:85787600-85789400	Active TSS	ES-I3 Cell Line	embryonic stem cell
23	chr2:85787600-85789400	Active TSS	H9 Cell Line	embryonic stem cell
24	chr2:85787600-85789400	Active TSS	HUES48 Cell Line	embryonic stem cell
25	chr2:85787600-85789400	Active TSS	HUES64 Cell Line	embryonic stem cell
26	chr2:85787600-85789400	Active TSS	iPS-18 Cell Line	embryonic stem cell
27	chr2:85787600-85789400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr2:85787600-85789600	Active TSS	Pancreatic Islets	Pancreatic Islet
29	chr2:85787800-85788400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
30	chr2:85787800-85788400	Flanking Active TSS	Primary B cells from cord blood	blood
31	chr2:85787800-85788400	Flanking Active TSS	Primary B cells from peripheral blood	blood
32	chr2:85787800-85788400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
33	chr2:85787800-85788400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
34	chr2:85787800-85788400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
35	chr2:85787800-85789000	Active TSS	Fetal Intestine Small	intestine
36	chr2:85787800-85789000	Active TSS	Lung	lung
37	chr2:85787800-85789200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr2:85787800-85789200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr2:85787800-85789200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr2:85787800-85789200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr2:85787800-85789200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr2:85787800-85789200	Active TSS	Muscle Satellite Cultured Cells	--
43	chr2:85787800-85789200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
44	chr2:85787800-85789200	Active TSS	Esophagus	oesophagus
45	chr2:85787800-85789200	Active TSS	Ovary	ovary
46	chr2:85787800-85789200	Active TSS	Thymus	Thymus
47	chr2:85787800-85789400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr2:85787800-85789400	Active TSS	Fetal Brain Female	brain
49	chr2:85787800-85789400	Active TSS	Fetal Kidney	kidney
50	chr2:85787800-85789400	Active TSS	Right Atrium	heart

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