Variant report

Variant	rs1078004
Chromosome Location	chr2:85769711-85769712
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:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:85579454..85586122-chr2:85763967..85769855,18	K562	blood:
2	chr2:85644216..85654950-chr2:85758513..85769717,70	MCF-7	breast:
3	chr2:85616263..85635094-chr2:85763849..85770697,56	MCF-7	breast:
4	chr2:85635544..85709381-chr2:85757395..85791508,633	K562	blood:
5	chr2:85729372..85732165-chr2:85769657..85772288,2	MCF-7	breast:
6	chr2:85609654..85691056-chr2:85759187..85790499,656	K562	blood:
7	chr2:85611082..85627761-chr2:85764356..85782623,83	K562	blood:
8	chr2:85716297..85718837-chr2:85769443..85771009,2	K562	blood:
9	chr2:85764346..85769986-chr2:85836202..85840842,10	MCF-7	breast:
10	chr2:85767293..85770194-chr2:85815993..85818775,2	MCF-7	breast:
11	chr2:85658029..85667242-chr2:85763719..85770665,19	MCF-7	breast:
12	chr2:85764454..85770994-chr2:85819148..85831427,14	K562	blood:
13	chr2:85642633..85666582-chr2:85757429..85771032,137	MCF-7	breast:
14	chr2:85617430..85626766-chr2:85763113..85771250,22	MCF-7	breast:
15	chr2:85766117..85770203-chr2:85837145..85839440,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000042445	Chromatin interaction
ENSG00000199936	Chromatin interaction
ENSG00000042493	Chromatin interaction
ENSG00000207207	Chromatin interaction
ENSG00000115459	Chromatin interaction
ENSG00000252293	Chromatin interaction
ENSG00000168890	Chromatin interaction
ENSG00000168887	Chromatin interaction
ENSG00000273196	Chromatin interaction
ENSG00000152292	Chromatin interaction
ENSG00000168883	Chromatin interaction
ENSG00000168894	Chromatin interaction
ENSG00000168899	Chromatin interaction
ENSG00000244399	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs1009	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs1010	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1011	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10172544	0.95[ASN][1000 genomes]
rs10175792	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10176176	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10179195	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]
rs10187424	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10198569	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10206961	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1058588	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11891260	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12473819	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12714145	0.95[ASN][1000 genomes]
rs13394343	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1348818	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs1446669	0.82[CHB][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs1561198	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1562323	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs17026396	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1972297	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2028898	0.86[CHB][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs2028900	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2043675	0.86[CHB][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs2044474	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2166529	0.92[CEU][hapmap];0.81[CHB][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2232748	0.81[JPT][hapmap]
rs2289972	0.86[CHB][hapmap];0.80[ASN][1000 genomes]
rs2366639	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2592551	0.86[CHB][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs2886722	0.81[CEU][hapmap];0.81[CHB][hapmap]
rs35215812	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3731827	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3731828	0.86[CHB][hapmap]
rs3755014	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3755015	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]
rs3770098	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs55971080	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59877521	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6547620	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6547621	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6547624	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6547629	0.80[JPT][hapmap]
rs6705839	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6705971	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]
rs6714157	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6714709	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6721924	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6731005	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6731700	0.80[ASN][1000 genomes]
rs6733550	0.80[JPT][hapmap]
rs6733913	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6735152	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6738009	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6738645	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6739015	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6743030	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6750832	0.90[ASN][1000 genomes]
rs6750847	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6757263	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs699664	0.86[CHB][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs7568458	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7579147	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs7591175	0.92[CEU][hapmap];0.82[CHB][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7593969	0.86[CHB][hapmap]
rs7605975	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs762684	0.86[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1078004	GGCX	cis	Whole Blood	GTEx
rs1078004	VAMP8	Cis_1M	lymphoblastoid	RTeQTL
rs1078004	GGCX	cis	Artery Tibial	GTEx
rs1078004	VAMP8	cis	multi-tissue	Pritchard
rs1078004	VAMP8	cis	Esophagus Mucosa	GTEx
rs1078004	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	chr2:85766400-85770200	Transcr. at gene 5' and 3'	Dnd41	blood
2	chr2:85766400-85770600	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
3	chr2:85766400-85770600	Transcr. at gene 5' and 3'	NHLF	lung
4	chr2:85766600-85770800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr2:85766800-85770000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr2:85766800-85770200	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
7	chr2:85766800-85770600	Transcr. at gene 5' and 3'	A549	lung
8	chr2:85767000-85769800	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
9	chr2:85767000-85770000	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
10	chr2:85767000-85770000	Transcr. at gene 5' and 3'	Brain Anterior Caudate	brain
11	chr2:85767000-85770200	Transcr. at gene 5' and 3'	Brain Hippocampus Middle	brain
12	chr2:85767000-85770200	Transcr. at gene 5' and 3'	NHEK	skin
13	chr2:85767000-85770400	Transcr. at gene 5' and 3'	K562	blood
14	chr2:85767000-85770600	Transcr. at gene 5' and 3'	HSMM	muscle
15	chr2:85767000-85771800	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr2:85767200-85769800	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr2:85767200-85770000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr2:85767200-85770200	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
19	chr2:85767200-85770400	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
20	chr2:85767200-85770600	Transcr. at gene 5' and 3'	Hela-S3	cervix
21	chr2:85767400-85769800	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
22	chr2:85767400-85770200	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr2:85767400-85770200	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr2:85767400-85770600	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
25	chr2:85767600-85769800	Transcr. at gene 5' and 3'	NH-A	brain
26	chr2:85767600-85770200	Transcr. at gene 5' and 3'	HMEC	breast
27	chr2:85767600-85770200	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
28	chr2:85767800-85769800	Transcr. at gene 5' and 3'	Brain Substantia Nigra	brain
29	chr2:85767800-85769800	Transcr. at gene 5' and 3'	HUVEC	blood vessel
30	chr2:85767800-85770400	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr2:85767800-85771000	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
32	chr2:85768200-85769800	Genic enhancers	Sigmoid Colon	Sigmoid Colon
33	chr2:85768200-85770000	Transcr. at gene 5' and 3'	Brain Angular Gyrus	brain
34	chr2:85768200-85770200	Transcr. at gene 5' and 3'	HSMMtube	muscle
35	chr2:85768400-85769800	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr2:85768400-85769800	Genic enhancers	Fetal Kidney	kidney
37	chr2:85768400-85769800	Transcr. at gene 5' and 3'	Thymus	Thymus
38	chr2:85768400-85770000	Transcr. at gene 5' and 3'	Skeletal Muscle Female	skeletal muscle
39	chr2:85768400-85770200	Transcr. at gene 5' and 3'	Brain Cingulate Gyrus	brain
40	chr2:85768400-85770200	Transcr. at gene 5' and 3'	Brain Dorsolateral Prefrontal Cortex	brain
41	chr2:85768400-85770400	Transcr. at gene 5' and 3'	Psoas Muscle	Psoas
42	chr2:85768400-85771400	Strong transcription	H9 Cell Line	embryonic stem cell
43	chr2:85768400-85773800	Strong transcription	Lung	lung
44	chr2:85768400-85774200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr2:85768400-85774800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr2:85768400-85774800	Strong transcription	Placenta Amnion	Placenta Amnion
47	chr2:85768400-85777000	Strong transcription	Placenta	Placenta
48	chr2:85768400-85778000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr2:85768400-85786600	Strong transcription	Fetal Muscle Trunk	muscle
50	chr2:85768600-85769800	Genic enhancers	ES-I3 Cell Line	embryonic stem cell

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