Variant report

Variant	rs1254898
Chromosome Location	chr2:85788140-85788141
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	SMC3	chr2:85787982-85788181	HepG2	liver:	n/a	n/a
2	SIN3AK20	chr2:85788028-85788384	H1-hESC	embryonic stem cell:	n/a	n/a
3	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
4	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
5	REST	chr2:85787879-85789264	H1-neurons	neurons:	n/a	n/a
6	TAF1	chr2:85788110-85789245	H1-hESC	embryonic stem cell:	n/a	n/a
7	CREB1	chr2:85787733-85789314	HepG2	liver:	n/a	n/a
8	RUNX3	chr2:85788002-85789357	GM12878	blood:	n/a	n/a
9	SIN3A	chr2:85788121-85789210	H1-hESC	embryonic stem cell:	n/a	chr2:85788727-85788738
10	TAF1	chr2:85788106-85789090	H1-neurons	neurons:	n/a	n/a
11	ZBTB7A	chr2:85788136-85789087	K562	blood:	n/a	n/a
12	CHD1	chr2:85788123-85788319	GM12878	blood:	n/a	n/a
13	YY1	chr2:85788102-85789255	K562	blood:	n/a	chr2:85788727-85788738 chr2:85788442-85788451 chr2:85788442-85788453 chr2:85788704-85788713 chr2:85788406-85788415
14	RAD21	chr2:85788132-85789101	IMR90	lung:	n/a	chr2:85788730-85788740
15	POLR2A	chr2:85786767-85789717	HepG2	liver:	n/a	n/a
16	HEY1	chr2:85788124-85789464	HepG2	liver:	n/a	n/a
17	TBL1XR1	chr2:85788108-85788274	K562	blood:	n/a	n/a
18	ELF1	chr2:85788092-85789090	GM12878	blood:	n/a	chr2:85788438-85788450 chr2:85788484-85788496
19	POLR2A	chr2:85788125-85789038	H1-neurons	neurons:	n/a	n/a
20	MXI1	chr2:85787838-85789269	IMR90	lung:	n/a	n/a
21	POLR2A	chr2:85788117-85789114	Hela-S3	cervix:	n/a	n/a
22	RCOR1	chr2:85787954-85789202	K562	blood:	n/a	n/a
23	MAFK	chr2:85788124-85788216	HepG2	liver:	n/a	n/a
24	POLR2A	chr2:85788084-85789304	PFSK-1	brain:	n/a	n/a
25	HDAC2	chr2:85788011-85788246	K562	blood:	n/a	n/a
26	RCOR1	chr2:85788007-85788207	K562	blood:	n/a	n/a
27	MAX	chr2:85788071-85789044	GM12878	blood:	n/a	chr2:85788404-85788414 chr2:85788407-85788417 chr2:85788727-85788737
28	BHLHE40	chr2:85788065-85788178	K562	blood:	n/a	n/a
29	MXI1	chr2:85787841-85788223	K562	blood:	n/a	n/a
30	EGR1	chr2:85788007-85788853	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
31	MYC	chr2:85788116-85789094	K562	blood:	n/a	chr2:85788404-85788414 chr2:85788407-85788417 chr2:85788727-85788737
32	MAFK	chr2:85788000-85788144	K562	blood:	n/a	n/a
33	ZBTB7A	chr2:85788110-85788974	ECC-1	luminal epithelium:	n/a	n/a
34	RUNX3	chr2:85788101-85789387	GM12878	blood:	n/a	n/a
35	JUN	chr2:85788015-85789463	K562	blood:	n/a	chr2:85788406-85788415 chr2:85788403-85788412 chr2:85788405-85788414
36	POLR2A	chr2:85788137-85789119	H1-neurons	neurons:	n/a	n/a
37	MAZ	chr2:85787722-85789231	IMR90	lung:	n/a	chr2:85788404-85788414 chr2:85788407-85788417 chr2:85788727-85788737

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	chr2:85787126..85789513-chr2:85826931..85829549,2	K562	blood:
11	chr2:85786233..85788829-chr2:85802669..85804855,3	K562	blood:
12	chr2:85552687..85556977-chr2:85784981..85789201,5	K562	blood:
13	chr2:85609654..85691056-chr2:85759187..85790499,656	K562	blood:
14	chr2:85784214..85789573-chr2:85827295..85831622,10	MCF-7	breast:
15	chr2:85771408..85781005-chr2:85784986..85791406,15	MCF-7	breast:
16	chr2:85765231..85769518-chr2:85784806..85790228,6	MCF-7	breast:
17	chr2:85539823..85542661-chr2:85786537..85789021,2	K562	blood:
18	chr2:85786233..85790202-chr2:85803177..85805521,3	K562	blood:
19	chr2:85787265..85788881-chr2:85843374..85845144,2	K562	blood:
20	chr2:85786482..85790460-chr2:85816178..85820132,9	MCF-7	breast:
21	chr2:85553459..85556724-chr2:85785432..85789140,4	MCF-7	breast:
22	chr2:85580977..85583407-chr2:85787270..85789639,2	MCF-7	breast:
23	chr2:85785973..85791563-chr2:85836230..85840689,7	MCF-7	breast:
24	chr2:85787036..85790013-chr2:85817133..85820348,4	MCF-7	breast:
25	chr2:85568800..85571035-chr2:85787413..85790410,2	MCF-7	breast:
26	chr2:85786921..85788482-chr2:85822883..85825336,2	MCF-7	breast:
27	chr2:85787502..85790371-chr2:85804560..85808548,6	MCF-7	breast:
28	chr2:85634213..85635735-chr2:85786387..85788534,2	MCF-7	breast:

Variant related genes	Relation type
VAMP8	TF binding region
ENSG00000168887	Chromatin interaction
ENSG00000042445	Chromatin interaction
ENSG00000115486	Chromatin interaction
ENSG00000199936	Chromatin interaction
ENSG00000252293	Chromatin interaction
ENSG00000168899	Chromatin interaction
ENSG00000042493	Chromatin interaction
ENSG00000118640	Chromatin interaction
ENSG00000168894	Chromatin interaction
ENSG00000207207	Chromatin interaction
ENSG00000244399	Chromatin interaction
ENSG00000115459	Chromatin interaction
ENSG00000152292	Chromatin interaction
ENSG00000246575	Chromatin interaction
ENSG00000152291	Chromatin interaction
ENSG00000273196	Chromatin interaction
ENSG00000168906	Chromatin interaction
ENSG00000168890	Chromatin interaction
ENSG00000168883	Chromatin interaction
ENSG00000270532	Chromatin interaction

Extended variants
information (count: 3 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs1254897	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1254901	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62164837	0.83[EUR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1254898	VAMP8	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85783200-85788200	Weak transcription	Small Intestine	intestine
2	chr2:85787000-85788200	Flanking Active TSS	Dnd41	blood
3	chr2:85787000-85789400	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr2:85787200-85788200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr2:85787200-85788200	Flanking Active TSS	Duodenum Mucosa	Duodenum
6	chr2:85787200-85789400	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr2:85787200-85789400	Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr2:85787200-85789400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr2:85787400-85788200	Flanking Active TSS	Rectal Smooth Muscle	rectum
10	chr2:85787400-85789000	Active TSS	Colonic Mucosa	Colon
11	chr2:85787400-85789200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr2:85787400-85789200	Active TSS	Pancreas	Pancrea
13	chr2:85787400-85789200	Bivalent/Poised TSS	HepG2	liver
14	chr2:85787400-85789400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr2:85787400-85789400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr2:85787400-85789400	Active TSS	Breast Myoepithelial Primary Cells	Breast
17	chr2:85787400-85789400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr2:85787400-85789400	Active TSS	A549	lung
19	chr2:85787400-85789400	Active TSS	HSMM	muscle
20	chr2:85787400-85789400	Active TSS	NHLF	lung
21	chr2:85787600-85788200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:85787600-85788200	Flanking Active TSS	Primary T cells from cord blood	blood
23	chr2:85787600-85788200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
24	chr2:85787600-85788200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
25	chr2:85787600-85788200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
26	chr2:85787600-85788200	Flanking Active TSS	Brain Cingulate Gyrus	brain
27	chr2:85787600-85788200	Flanking Active TSS	Brain Germinal Matrix	brain
28	chr2:85787600-85788200	Flanking Active TSS	Brain Hippocampus Middle	brain
29	chr2:85787600-85788200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
30	chr2:85787600-85788200	Flanking Active TSS	Colon Smooth Muscle	Colon
31	chr2:85787600-85788200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
32	chr2:85787600-85788200	Flanking Active TSS	Fetal Muscle Leg	muscle
33	chr2:85787600-85788200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
34	chr2:85787600-85788200	Flanking Active TSS	HUVEC	blood vessel
35	chr2:85787600-85788200	Flanking Active TSS	NHEK	skin
36	chr2:85787600-85788400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr2:85787600-85788400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr2:85787600-85788400	Flanking Active TSS	Adipose Nuclei	Adipose
39	chr2:85787600-85789200	Active TSS	H1 Cell Line	embryonic stem cell
40	chr2:85787600-85789200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr2:85787600-85789200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr2:85787600-85789400	Active TSS	ES-I3 Cell Line	embryonic stem cell
43	chr2:85787600-85789400	Active TSS	H9 Cell Line	embryonic stem cell
44	chr2:85787600-85789400	Active TSS	HUES48 Cell Line	embryonic stem cell
45	chr2:85787600-85789400	Active TSS	HUES64 Cell Line	embryonic stem cell
46	chr2:85787600-85789400	Active TSS	iPS-18 Cell Line	embryonic stem cell
47	chr2:85787600-85789400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr2:85787600-85789600	Active TSS	Pancreatic Islets	Pancreatic Islet
49	chr2:85787800-85788200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
50	chr2:85787800-85788200	Flanking Active TSS	Primary hematopoietic stem cells	blood

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