Variant report

Variant	rs6743030
Chromosome Location	chr2:85763520-85763521
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	POLR2A	chr2:85763345-85763535	H1-hESC	embryonic stem cell:	n/a	n/a
2	GATA2	chr2:85763497-85763892	SH-SY5Y	brain:	n/a	n/a
3	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
4	EP300	chr2:85763516-85763888	SK-N-SH_RA	brain:	n/a	n/a
5	MXI1	chr2:85763373-85768685	SK-N-SH	brain:	n/a	chr2:85766928-85766937
6	GATA3	chr2:85763519-85763981	SH-SY5Y	brain:	n/a	n/a
7	POLR2A	chr2:85763347-85763955	PANC-1	pancreas:	n/a	n/a
8	JUND	chr2:85763443-85767859	SK-N-SH	brain:	n/a	chr2:85765583-85765592 chr2:85765508-85765522 chr2:85766871-85766880 chr2:85765968-85765977
9	POLR2A	chr2:85763504-85763892	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:85644216..85654950-chr2:85758513..85769717,70	MCF-7	breast:
2	chr2:85663253..85664901-chr2:85761571..85763604,2	MCF-7	breast:
3	chr2:85699337..85700838-chr2:85763015..85764537,2	K562	blood:
4	chr2:85763361..85766337-chr6:3257277..3259286,2	MCF-7	breast:
5	chr2:85579256..85583791-chr2:85762380..85768080,8	MCF-7	breast:
6	chr2:85637558..85640126-chr2:85762094..85764300,2	MCF-7	breast:
7	chr2:85549396..85557177-chr2:85763484..85769653,16	MCF-7	breast:
8	chr2:85702779..85705594-chr2:85762118..85763957,2	K562	blood:
9	chr2:85593223..85597895-chr2:85762999..85767407,5	K562	blood:
10	chr2:85676312..85679045-chr2:85763081..85764997,2	MCF-7	breast:
11	chr2:85635544..85709381-chr2:85757395..85791508,633	K562	blood:
12	chr2:85609654..85691056-chr2:85759187..85790499,656	K562	blood:
13	chr2:85627012..85628603-chr2:85761794..85764774,2	MCF-7	breast:
14	chr2:85551607..85557241-chr2:85763492..85768403,12	K562	blood:
15	chr2:85642633..85666582-chr2:85757429..85771032,137	MCF-7	breast:
16	chr2:85617430..85626766-chr2:85763113..85771250,22	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GGCX-3	chr2:85763511-85763800	NONHSAT072013

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

Extended variants
information (count: 59 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1010	0.85[ASN][1000 genomes]
rs1011	0.86[ASN][1000 genomes]
rs10172544	0.93[ASN][1000 genomes]
rs10175792	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10176176	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10179195	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10187424	0.88[ASN][1000 genomes]
rs10198569	0.88[ASN][1000 genomes]
rs10206961	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1058588	0.86[ASN][1000 genomes]
rs1078004	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11891260	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11895341	0.81[ASN][1000 genomes]
rs11895399	0.81[ASN][1000 genomes]
rs11895401	0.81[ASN][1000 genomes]
rs12473819	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12714145	0.93[ASN][1000 genomes]
rs13394343	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1446669	0.81[ASN][1000 genomes]
rs1561198	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1562323	0.86[ASN][1000 genomes]
rs17026396	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1972297	0.86[ASN][1000 genomes]
rs2028900	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2044474	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2166529	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2366639	0.86[ASN][1000 genomes]
rs35215812	0.90[ASN][1000 genomes]
rs3731827	0.86[ASN][1000 genomes]
rs3755014	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3755015	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3770098	0.85[ASN][1000 genomes]
rs55971080	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56819945	0.81[ASN][1000 genomes]
rs59877521	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6547620	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6547621	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6547624	0.85[ASN][1000 genomes]
rs6705839	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6705971	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6714157	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6714709	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6721924	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6722691	0.81[ASN][1000 genomes]
rs6731005	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6731700	0.81[ASN][1000 genomes]
rs6733913	0.82[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	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6738645	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6739015	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6750832	0.90[ASN][1000 genomes]
rs6750847	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6757263	0.86[ASN][1000 genomes]
rs7568458	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7591175	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7605975	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6743030	VAMP8	cis	multi-tissue	Pritchard
rs6743030	VAMP8	Cis_1M	lymphoblastoid	RTeQTL
rs6743030	VAMP8	cis	Esophagus Mucosa	GTEx
rs6743030	GGCX	cis	Whole Blood	GTEx

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85745000-85764800	Weak transcription	Esophagus	oesophagus
2	chr2:85751200-85764000	Weak transcription	Psoas Muscle	Psoas
3	chr2:85751200-85764400	Weak transcription	Small Intestine	intestine
4	chr2:85752000-85764800	Weak transcription	Gastric	stomach
5	chr2:85752400-85764800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:85752600-85763600	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr2:85753000-85764000	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr2:85758200-85764800	Enhancers	Primary neutrophils fromperipheralblood	blood
9	chr2:85758600-85764200	Weak transcription	Duodenum Mucosa	Duodenum
10	chr2:85759200-85764000	Weak transcription	Liver	Liver
11	chr2:85760800-85764000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr2:85761200-85764400	Enhancers	Stomach Mucosa	stomach
13	chr2:85761400-85764400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr2:85761400-85764600	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr2:85761400-85764600	Enhancers	Primary hematopoietic stem cells	blood
16	chr2:85761600-85764600	Enhancers	Fetal Intestine Small	intestine
17	chr2:85761800-85763600	Weak transcription	Fetal Intestine Large	intestine
18	chr2:85761800-85763600	Weak transcription	Rectal Smooth Muscle	rectum
19	chr2:85761800-85763600	Weak transcription	NHEK	skin
20	chr2:85761800-85764000	Weak transcription	GM12878-XiMat	blood
21	chr2:85762000-85764200	Enhancers	Brain Anterior Caudate	brain
22	chr2:85762000-85764200	Enhancers	A549	lung
23	chr2:85762000-85764400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr2:85762200-85763600	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr2:85762200-85763800	Weak transcription	Brain Hippocampus Middle	brain
26	chr2:85762400-85764200	Enhancers	Hela-S3	cervix
27	chr2:85762600-85763600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr2:85762600-85764200	Weak transcription	Primary B cells from cord blood	blood
29	chr2:85762600-85764200	Enhancers	NHDF-Ad	bronchial
30	chr2:85762800-85764000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr2:85762800-85764000	Weak transcription	K562	blood
32	chr2:85762800-85764200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr2:85762800-85764200	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr2:85763000-85763600	Weak transcription	Brain Cingulate Gyrus	brain
35	chr2:85763000-85763800	Weak transcription	Thymus	Thymus
36	chr2:85763000-85764200	Enhancers	Osteobl	bone
37	chr2:85763200-85763600	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr2:85763200-85763800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr2:85763400-85763600	Enhancers	Muscle Satellite Cultured Cells	--
40	chr2:85763400-85763600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr2:85763400-85763600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr2:85763400-85763600	Enhancers	HSMM	muscle
43	chr2:85763400-85763800	Flanking Active TSS	HSMMtube	muscle
44	chr2:85763400-85764000	Enhancers	Pancreas	Pancrea
45	chr2:85763400-85764200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr2:85763400-85764200	Enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr2:85763400-85764200	Enhancers	Brain Angular Gyrus	brain
48	chr2:85763400-85764200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
49	chr2:85763400-85764200	Enhancers	Colon Smooth Muscle	Colon
50	chr2:85763400-85764200	Genic enhancers	Dnd41	blood

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