Variant report

Variant	rs3755015
Chromosome Location	chr2:85764041-85764042
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:21)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr2:85763716-85764048	MCF10A-Er-Src	breast:	n/a	n/a
2	REST	chr2:85763518-85767607	H1-neurons	neurons:	n/a	chr2:85766116-85766129 chr2:85766157-85766170 chr2:85766157-85766170 chr2:85766274-85766287 chr2:85765620-85765628 chr2:85764843-85764856
3	SREBP1	chr2:85763798-85768460	GM12878	blood:	n/a	n/a
4	CTCF	chr2:85763722-85768035	A549	lung:	n/a	n/a
5	GATA1	chr2:85763765-85764270	PBDE	blood:	n/a	n/a
6	MXI1	chr2:85763373-85768685	SK-N-SH	brain:	n/a	chr2:85766928-85766937
7	ARID3A	chr2:85763601-85764174	K562	blood:	n/a	n/a
8	POLR2A	chr2:85763721-85768325	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr2:85763566-85764073	U87	brain:	n/a	n/a
10	POLR2A	chr2:85763991-85776489	H1-hESC	embryonic stem cell:	n/a	n/a
11	JUND	chr2:85763443-85767859	SK-N-SH	brain:	n/a	chr2:85765583-85765592 chr2:85765508-85765522 chr2:85766871-85766880 chr2:85765968-85765977

No data

(count:21 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:85551217..85557082-chr2:85763566..85768403,18	K562	blood:
2	chr2:85579454..85586122-chr2:85763967..85769855,18	K562	blood:
3	chr2:85644216..85654950-chr2:85758513..85769717,70	MCF-7	breast:
4	chr2:85699337..85700838-chr2:85763015..85764537,2	K562	blood:
5	chr2:85763361..85766337-chr6:3257277..3259286,2	MCF-7	breast:
6	chr2:85579256..85583791-chr2:85762380..85768080,8	MCF-7	breast:
7	chr2:85637558..85640126-chr2:85762094..85764300,2	MCF-7	breast:
8	chr2:85549396..85557177-chr2:85763484..85769653,16	MCF-7	breast:
9	chr2:85616263..85635094-chr2:85763849..85770697,56	MCF-7	breast:
10	chr2:85593223..85597895-chr2:85762999..85767407,5	K562	blood:
11	chr2:85676312..85679045-chr2:85763081..85764997,2	MCF-7	breast:
12	chr2:85635544..85709381-chr2:85757395..85791508,633	K562	blood:
13	chr2:85764018..85768553-chr2:85822883..85829718,12	MCF-7	breast:
14	chr2:85684691..85688557-chr2:85764007..85767922,5	MCF-7	breast:
15	chr2:85609654..85691056-chr2:85759187..85790499,656	K562	blood:
16	chr2:85627012..85628603-chr2:85761794..85764774,2	MCF-7	breast:
17	chr2:85658029..85667242-chr2:85763719..85770665,19	MCF-7	breast:
18	chr2:85551607..85557241-chr2:85763492..85768403,12	K562	blood:
19	chr2:85642633..85666582-chr2:85757429..85771032,137	MCF-7	breast:
20	chr2:85617430..85626766-chr2:85763113..85771250,22	MCF-7	breast:
21	chr2:85763670..85765821-chr8:103626482..103628090,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GGCX-3	chr2:85763939-85766100	NONHSAT072013

No data

Variant related genes	Relation type
MAT2A	TF binding region
RN7SL830P	TF binding region
ENSG00000042445	Chromatin interaction
ENSG00000252293	Chromatin interaction
ENSG00000242095	Chromatin interaction
ENSG00000042493	Chromatin interaction
ENSG00000152292	Chromatin interaction
ENSG00000152291	Chromatin interaction
ENSG00000207207	Chromatin interaction
ENSG00000168890	Chromatin interaction
ENSG00000202382	Chromatin interaction
ENSG00000168894	Chromatin interaction
ENSG00000273196	Chromatin interaction
ENSG00000244399	Chromatin interaction
ENSG00000115459	Chromatin interaction
ENSG00000180822	Chromatin interaction
ENSG00000199936	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1009	0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs1010	0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs1011	0.87[ASN][1000 genomes]
rs10172544	0.94[ASN][1000 genomes]
rs10175792	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10176176	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10179195	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10187424	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10198569	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10206961	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1058588	0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs1078004	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11891260	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12473819	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12714145	0.94[ASN][1000 genomes]
rs13394343	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1348818	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs1446669	0.86[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs1561198	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1562323	0.87[ASN][1000 genomes]
rs17026396	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1972297	0.87[ASN][1000 genomes]
rs2028898	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs2028900	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2043675	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs2044474	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2166529	0.92[CEU][hapmap];0.86[CHB][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2232748	0.81[JPT][hapmap]
rs2289972	0.90[CHB][hapmap]
rs2366639	0.87[ASN][1000 genomes]
rs2592551	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs2886722	0.86[CHB][hapmap]
rs35215812	0.91[ASN][1000 genomes]
rs3731827	0.87[ASN][1000 genomes]
rs3731828	0.90[CHB][hapmap]
rs3755014	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3770098	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs55971080	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59877521	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6547620	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6547621	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6547624	0.86[ASN][1000 genomes]
rs6547629	0.80[JPT][hapmap]
rs6705839	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6705971	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6714157	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6714709	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6721924	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6731005	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6731700	0.81[ASN][1000 genomes]
rs6733550	0.80[JPT][hapmap]
rs6733913	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6735152	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6738009	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6738645	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6739015	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6743030	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6750832	0.91[ASN][1000 genomes]
rs6750847	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6757263	0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs699664	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs7568458	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7579147	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs7591175	0.93[CEU][hapmap];0.87[CHB][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7593969	0.90[CHB][hapmap]
rs7605975	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs762684	0.91[CHB][hapmap];0.86[JPT][hapmap]

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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs3755015	VAMP8	cis	Esophagus Mucosa	GTEx
rs3755015	VAMP8	cis	multi-tissue	Pritchard
rs3755015	GGCX	cis	Artery Aorta	GTEx
rs3755015	VAMP8	Cis_1M	lymphoblastoid	RTeQTL
rs3755015	GGCX	cis	Artery Tibial	GTEx
rs3755015	VAMP8	cis	uninvolved skin	skin_eQTL
rs3755015	VAMP8	cis	lesional skin	skin_eQTL
rs3755015	GGCX	cis	Whole Blood	GTEx

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85745000-85764800	Weak transcription	Esophagus	oesophagus
2	chr2:85751200-85764400	Weak transcription	Small Intestine	intestine
3	chr2:85752000-85764800	Weak transcription	Gastric	stomach
4	chr2:85752400-85764800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:85758200-85764800	Enhancers	Primary neutrophils fromperipheralblood	blood
6	chr2:85758600-85764200	Weak transcription	Duodenum Mucosa	Duodenum
7	chr2:85761200-85764400	Enhancers	Stomach Mucosa	stomach
8	chr2:85761400-85764400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr2:85761400-85764600	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr2:85761400-85764600	Enhancers	Primary hematopoietic stem cells	blood
11	chr2:85761600-85764600	Enhancers	Fetal Intestine Small	intestine
12	chr2:85762000-85764200	Enhancers	Brain Anterior Caudate	brain
13	chr2:85762000-85764200	Enhancers	A549	lung
14	chr2:85762000-85764400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr2:85762400-85764200	Enhancers	Hela-S3	cervix
16	chr2:85762600-85764200	Weak transcription	Primary B cells from cord blood	blood
17	chr2:85762600-85764200	Enhancers	NHDF-Ad	bronchial
18	chr2:85762800-85764200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr2:85762800-85764200	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr2:85763000-85764200	Enhancers	Osteobl	bone
21	chr2:85763400-85764200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr2:85763400-85764200	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr2:85763400-85764200	Enhancers	Brain Angular Gyrus	brain
24	chr2:85763400-85764200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
25	chr2:85763400-85764200	Enhancers	Colon Smooth Muscle	Colon
26	chr2:85763400-85764200	Genic enhancers	Dnd41	blood
27	chr2:85763400-85764200	Enhancers	NH-A	brain
28	chr2:85763400-85764400	Enhancers	Brain Substantia Nigra	brain
29	chr2:85763400-85764400	Enhancers	Duodenum Smooth Muscle	Duodenum
30	chr2:85763400-85764800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr2:85763600-85764200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr2:85763600-85764200	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr2:85763600-85764200	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr2:85763600-85764200	Enhancers	Brain Cingulate Gyrus	brain
35	chr2:85763600-85764200	Enhancers	Brain Germinal Matrix	brain
36	chr2:85763600-85764200	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr2:85763600-85764200	Enhancers	Rectal Mucosa Donor 29	rectum
38	chr2:85763600-85764200	Enhancers	Rectal Smooth Muscle	rectum
39	chr2:85763600-85764200	Enhancers	HMEC	breast
40	chr2:85763600-85764200	Enhancers	NHEK	skin
41	chr2:85763600-85764400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr2:85763600-85764400	Enhancers	HUVEC	blood vessel
43	chr2:85763600-85764400	Enhancers	Monocytes-CD14+_RO01746	blood
44	chr2:85763600-85764400	Enhancers	NHLF	lung
45	chr2:85763600-85764600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr2:85763600-85764600	Enhancers	Primary T helper cells PMA-I stimulated	--
47	chr2:85763600-85764600	Enhancers	Fetal Intestine Large	intestine
48	chr2:85763600-85764800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr2:85763600-85765000	Enhancers	Fetal Heart	heart
50	chr2:85763600-85765000	Flanking Active TSS	HSMM	muscle

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