Variant report

Variant	rs1254897
Chromosome Location	chr2:85786556-85786557
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:85644876..85649493-chr2:85786296..85791442,7	MCF-7	breast:
2	chr2:85644868..85648304-chr2:85783356..85788933,7	MCF-7	breast:
3	chr2:85635544..85709381-chr2:85757395..85791508,633	K562	blood:
4	chr2:85785429..85790468-chr2:85820934..85826927,9	MCF-7	breast:
5	chr2:85786233..85788829-chr2:85802669..85804855,3	K562	blood:
6	chr2:85552687..85556977-chr2:85784981..85789201,5	K562	blood:
7	chr2:85609654..85691056-chr2:85759187..85790499,656	K562	blood:
8	chr2:85784214..85789573-chr2:85827295..85831622,10	MCF-7	breast:
9	chr2:85771408..85781005-chr2:85784986..85791406,15	MCF-7	breast:
10	chr2:85765231..85769518-chr2:85784806..85790228,6	MCF-7	breast:
11	chr2:85539823..85542661-chr2:85786537..85789021,2	K562	blood:
12	chr2:85786233..85790202-chr2:85803177..85805521,3	K562	blood:
13	chr2:85786482..85790460-chr2:85816178..85820132,9	MCF-7	breast:
14	chr2:85553459..85556724-chr2:85785432..85789140,4	MCF-7	breast:
15	chr2:85785973..85791563-chr2:85836230..85840689,7	MCF-7	breast:
16	chr2:85634213..85635735-chr2:85786387..85788534,2	MCF-7	breast:

No data

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

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

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

rs_ID	r²[population]
rs1254898	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1254901	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62164837	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1254897	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	chr2:85768400-85786600	Strong transcription	Fetal Muscle Trunk	muscle
2	chr2:85769400-85786600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:85769400-85786600	Strong transcription	Brain Germinal Matrix	brain
4	chr2:85769400-85787800	Weak transcription	Right Atrium	heart
5	chr2:85769800-85787000	Strong transcription	Fetal Stomach	stomach
6	chr2:85769800-85788000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr2:85770200-85787800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr2:85770600-85786600	Strong transcription	Fetal Brain Female	brain
9	chr2:85772000-85786600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr2:85775600-85786600	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr2:85776600-85787000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr2:85777000-85787200	Strong transcription	NHEK	skin
13	chr2:85777200-85786600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr2:85778200-85787000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr2:85779200-85787200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr2:85779400-85786600	Strong transcription	Primary B cells from peripheral blood	blood
17	chr2:85779600-85786600	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr2:85779600-85787000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr2:85779600-85787000	Strong transcription	Fetal Muscle Leg	muscle
20	chr2:85779600-85787600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr2:85780200-85787200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr2:85780400-85787000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr2:85781600-85787000	Weak transcription	Fetal Heart	heart
24	chr2:85781600-85787000	Weak transcription	Stomach Mucosa	stomach
25	chr2:85782000-85787800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr2:85782400-85787600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr2:85782400-85787600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr2:85782400-85787600	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr2:85782600-85787200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr2:85782600-85787600	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr2:85782600-85787800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr2:85782800-85787800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr2:85782800-85788000	Weak transcription	Aorta	Aorta
34	chr2:85783000-85787800	Weak transcription	Ovary	ovary
35	chr2:85783200-85788200	Weak transcription	Small Intestine	intestine
36	chr2:85783400-85787200	Weak transcription	Colonic Mucosa	Colon
37	chr2:85783600-85787200	Weak transcription	Primary B cells from cord blood	blood
38	chr2:85784000-85786800	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr2:85784000-85787000	Weak transcription	NHDF-Ad	bronchial
40	chr2:85784200-85787000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr2:85785400-85786600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
42	chr2:85785600-85786800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr2:85785600-85787000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr2:85785600-85787000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr2:85785800-85787000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr2:85785800-85787000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr2:85785800-85787000	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr2:85785800-85787000	Weak transcription	Psoas Muscle	Psoas
49	chr2:85785800-85787200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr2:85785800-85787200	Weak transcription	Right Ventricle	heart

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