Variant report

Variant	rs62165899
Chromosome Location	chr2:85772628-85772629
allele	C/T
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:39)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:39 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:85724612..85727144-chr2:85772474..85775148,2	K562	blood:
2	chr2:85771530..85776249-chr2:85829549..85833813,5	K562	blood:
3	chr2:85705123..85709274-chr2:85772334..85776338,4	K562	blood:
4	chr2:85645994..85650779-chr2:85769890..85775374,14	MCF-7	breast:
5	chr2:85772535..85775782-chr2:85811298..85814836,3	MCF-7	breast:
6	chr2:85772605..85778348-chr2:85801967..85806164,7	K562	blood:
7	chr2:85623550..85625487-chr2:85771824..85773837,2	MCF-7	breast:
8	chr2:85771408..85781005-chr2:85784986..85791406,15	MCF-7	breast:
9	chr2:85695182..85700475-chr2:85771258..85775492,7	K562	blood:
10	chr2:85772489..85775609-chr2:85830243..85835549,6	MCF-7	breast:
11	chr2:85557851..85560979-chr2:85771995..85775523,3	K562	blood:
12	chr2:85726132..85728834-chr2:85772359..85774217,2	K562	blood:
13	chr2:85635544..85709381-chr2:85757395..85791508,633	K562	blood:
14	chr2:85632185..85634423-chr2:85770143..85772992,3	K562	blood:
15	chr2:85691531..85694177-chr2:85771746..85774337,2	K562	blood:
16	chr2:85734096..85736580-chr2:85771521..85774702,3	K562	blood:
17	chr2:85641902..85652165-chr2:85771116..85782225,51	MCF-7	breast:
18	chr2:85681701..85683318-chr2:85770931..85773201,2	MCF-7	breast:
19	chr2:85615286..85623438-chr2:85771409..85780547,22	MCF-7	breast:
20	chr2:85609654..85691056-chr2:85759187..85790499,656	K562	blood:
21	chr2:85611082..85627761-chr2:85764356..85782623,83	K562	blood:
22	chr2:85653033..85655278-chr2:85772397..85774783,3	MCF-7	breast:
23	chr2:85771440..85773925-chr2:85797932..85801717,3	K562	blood:
24	chr2:85643598..85645785-chr2:85770608..85772965,2	MCF-7	breast:
25	chr2:85579680..85582671-chr2:85771028..85773256,2	K562	blood:
26	chr2:85734925..85738483-chr2:85772502..85775940,3	MCF-7	breast:
27	chr2:85602211..85604974-chr2:85772434..85774116,2	K562	blood:
28	chr2:85771249..85774219-chr2:85842465..85844960,3	MCF-7	breast:
29	chr19:19496724..19499186-chr2:85772570..85774363,2	K562	blood:
30	chr19:56185306..56186143-chr2:85772139..85772918,2	Hela-S3	cervix:
31	chr2:85771229..85776857-chr2:85808442..85817073,8	K562	blood:
32	chr2:85730345..85732165-chr2:85772165..85774590,2	K562	blood:
33	chr2:85596461..85599637-chr2:85772544..85775880,4	K562	blood:
34	chr2:85589339..85593545-chr2:85771019..85776270,4	K562	blood:
35	chr2:85615241..85625394-chr2:85772377..85782714,25	MCF-7	breast:
36	chr17:41438071..41438607-chr2:85772186..85772937,2	Hela-S3	cervix:
37	chr2:85601232..85604311-chr2:85772616..85776174,4	K562	blood:
38	chr2:85729360..85731940-chr2:85770278..85775581,5	K562	blood:
39	chr2:85771530..85774083-chr2:85838738..85840768,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000244399	Chromatin interaction
ENSG00000042445	Chromatin interaction
ENSG00000167491	Chromatin interaction
ENSG00000118640	Chromatin interaction
ENSG00000042493	Chromatin interaction
ENSG00000252293	Chromatin interaction
ENSG00000207207	Chromatin interaction
ENSG00000267523	Chromatin interaction
ENSG00000168890	Chromatin interaction
ENSG00000273196	Chromatin interaction
ENSG00000168899	Chromatin interaction
ENSG00000152292	Chromatin interaction
ENSG00000115486	Chromatin interaction
ENSG00000199936	Chromatin interaction
ENSG00000168887	Chromatin interaction
ENSG00000239143	Chromatin interaction
ENSG00000115459	Chromatin interaction
ENSG00000168883	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10166612	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10167018	0.96[ASN][1000 genomes]
rs10172793	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10174551	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10179904	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10187218	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10190585	0.96[ASN][1000 genomes]
rs10196357	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10198001	0.87[ASN][1000 genomes]
rs10198761	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10202828	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10496316	0.96[ASN][1000 genomes]
rs12714142	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12714143	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12714144	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12714146	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12714147	0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12994163	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13000511	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13387999	0.86[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs13394092	0.86[ASN][1000 genomes]
rs13406611	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13406935	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13408713	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13409377	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13421434	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13425821	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13426038	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13429968	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13431159	0.86[ASN][1000 genomes]
rs13431962	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13432584	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17430670	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17508727	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17735885	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2121397	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28398892	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28479378	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28564788	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28800839	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28810460	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34212016	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34214220	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34565621	0.85[AMR][1000 genomes]
rs34669893	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34824628	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35776719	0.85[ASN][1000 genomes]
rs55892665	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56359002	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62165905	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62165907	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6727614	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005351	chr2:85242657-85774909	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	198 gene(s)	inside rSNPs	diseases
2	nsv535803	chr2:85242657-85774909	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	198 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62165899	VAMP5	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85768400-85773800	Strong transcription	Lung	lung
2	chr2:85768400-85774200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr2:85768400-85774800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr2:85768400-85774800	Strong transcription	Placenta Amnion	Placenta Amnion
5	chr2:85768400-85777000	Strong transcription	Placenta	Placenta
6	chr2:85768400-85778000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr2:85768400-85786600	Strong transcription	Fetal Muscle Trunk	muscle
8	chr2:85768600-85773200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr2:85768600-85773200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr2:85768600-85774600	Strong transcription	Primary B cells from peripheral blood	blood
11	chr2:85768600-85779000	Strong transcription	Primary T cells fromperipheralblood	blood
12	chr2:85768600-85786200	Strong transcription	Fetal Thymus	thymus
13	chr2:85768800-85773600	Strong transcription	Spleen	Spleen
14	chr2:85768800-85773800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr2:85769000-85773000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr2:85769000-85773400	Strong transcription	Ovary	ovary
17	chr2:85769000-85774200	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr2:85769200-85772800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr2:85769200-85773000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
20	chr2:85769200-85774400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr2:85769200-85774600	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr2:85769200-85774800	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr2:85769400-85773200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
24	chr2:85769400-85773200	Strong transcription	Colonic Mucosa	Colon
25	chr2:85769400-85774000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
26	chr2:85769400-85775800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr2:85769400-85776000	Strong transcription	Primary T cells from cord blood	blood
28	chr2:85769400-85776200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr2:85769400-85777000	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr2:85769400-85782800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr2:85769400-85786600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr2:85769400-85786600	Strong transcription	Brain Germinal Matrix	brain
33	chr2:85769400-85787800	Weak transcription	Right Atrium	heart
34	chr2:85769600-85773000	Genic enhancers	Stomach Smooth Muscle	stomach
35	chr2:85769600-85773400	Strong transcription	H1 Cell Line	embryonic stem cell
36	chr2:85769800-85773000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr2:85769800-85773200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
38	chr2:85769800-85773200	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr2:85769800-85773200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr2:85769800-85773400	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr2:85769800-85773600	Strong transcription	Fetal Kidney	kidney
42	chr2:85769800-85775000	Strong transcription	Sigmoid Colon	Sigmoid Colon
43	chr2:85769800-85777200	Strong transcription	Adipose Nuclei	Adipose
44	chr2:85769800-85779400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr2:85769800-85782800	Strong transcription	Thymus	Thymus
46	chr2:85769800-85786400	Strong transcription	HUES6 Cell Line	embryonic stem cell
47	chr2:85769800-85787000	Strong transcription	Fetal Stomach	stomach
48	chr2:85769800-85788000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
49	chr2:85770000-85772800	Strong transcription	Right Ventricle	heart
50	chr2:85770000-85773400	Genic enhancers	Skeletal Muscle Female	skeletal muscle

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