Variant report

Variant	rs2066818
Chromosome Location	chr12:56753822-56753823
allele	G/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:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:56748050..56751002-chr12:56753460..56756305,2	K562	blood:
2	chr12:56707405..56709200-chr12:56752769..56755378,2	MCF-7	breast:
3	chr12:56752493..56755436-chr12:56859728..56862331,2	MCF-7	breast:
4	chr12:56752523..56755343-chr12:56862151..56864248,2	MCF-7	breast:
5	chr12:56752238..56754707-chr12:56756251..56758252,3	MCF-7	breast:
6	chr12:56743017..56746738-chr12:56752337..56755444,3	K562	blood:
7	chr12:56727184..56732099-chr12:56751309..56755132,9	K562	blood:
8	chr12:56751886..56753976-chr12:56841675..56844416,2	MCF-7	breast:
9	chr12:56725978..56729877-chr12:56750632..56755261,5	MCF-7	breast:
10	chr12:56747914..56751304-chr12:56752091..56755313,3	MCF-7	breast:
11	chr12:56692915..56694824-chr12:56751015..56754096,3	MCF-7	breast:
12	chr12:56726126..56729287-chr12:56751281..56753885,4	MCF-7	breast:
13	chr12:56709376..56709962-chr12:56753438..56754246,2	MCF-7	breast:
14	chr12:56753366..56754007-chr22:50968209..50969038,2	Hela-S3	cervix:
15	chr12:56752241..56754348-chr12:56862536..56866569,3	K562	blood:
16	chr12:56748502..56750410-chr12:56752086..56754336,2	MCF-7	breast:
17	chr12:56582084..56583845-chr12:56753291..56755155,2	MCF-7	breast:
18	chr12:56582392..56584464-chr12:56753681..56756139,2	MCF-7	breast:
19	chr12:56753203..56755632-chr12:56841567..56843289,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000257727	Chromatin interaction
ENSG00000144785	Chromatin interaction
ENSG00000139613	Chromatin interaction
ENSG00000135423	Chromatin interaction
ENSG00000176422	Chromatin interaction
ENSG00000025708	Chromatin interaction
ENSG00000135473	Chromatin interaction
ENSG00000170581	Chromatin interaction
ENSG00000175336	Chromatin interaction
ENSG00000062485	Chromatin interaction
ENSG00000252206	Chromatin interaction
ENSG00000135517	Chromatin interaction
ENSG00000257303	Chromatin interaction
ENSG00000111602	Chromatin interaction
ENSG00000258199	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10876882	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs11171803	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11171806	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11575224	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11575229	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11575231	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11575232	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11575234	0.94[EUR][1000 genomes]
rs11575248	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1274493	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes]
rs17118403	0.89[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs17118409	0.89[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17118431	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17118439	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1802236	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2020854	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs2066807	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2066808	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[EUR][1000 genomes]
rs2066819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2291361	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2306693	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2306694	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2371454	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2371494	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[EUR][1000 genomes]
rs2629447	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs2643626	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[EUR][1000 genomes]
rs2695782	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[EUR][1000 genomes]
rs2695788	0.88[EUR][1000 genomes]
rs2695789	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[EUR][1000 genomes]
rs35526714	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs41363748	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs41392645	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs41423244	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs57137641	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs57279772	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs57343616	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs57367440	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57870697	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58852079	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59295315	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59626664	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs59811639	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59822547	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs59917308	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs60192809	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs60542959	0.84[EUR][1000 genomes]
rs60913149	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs703830	0.88[EUR][1000 genomes]
rs744051	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs773652	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes]
rs773664	0.88[EUR][1000 genomes]
rs773665	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[EUR][1000 genomes]
rs808919	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs871130	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][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	nsv1043622	chr12:56571476-56974448	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
2	nsv541500	chr12:56571476-56974448	Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2066818	RP11-977G19.11	cis	Artery Tibial	GTEx
rs2066818	TMEM4	Cis_1M	lymphoblastoid	RTeQTL
rs2066818	RP11-977G19.11	cis	Artery Aorta	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56751600-56755000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr12:56751600-56755000	Active TSS	GM12878-XiMat	blood
3	chr12:56752000-56754800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr12:56752200-56755000	Active TSS	HSMMtube	muscle
5	chr12:56752400-56754800	Active TSS	Duodenum Smooth Muscle	Duodenum
6	chr12:56752400-56754800	Active TSS	Sigmoid Colon	Sigmoid Colon
7	chr12:56752400-56755000	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr12:56752400-56755200	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr12:56752400-56755200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr12:56752400-56755200	Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr12:56752400-56755600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr12:56752600-56754600	Active TSS	Fetal Muscle Trunk	muscle
13	chr12:56752600-56754800	Active TSS	Aorta	Aorta
14	chr12:56752600-56755000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr12:56752600-56755000	Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr12:56752600-56755200	Active TSS	iPS-18 Cell Line	embryonic stem cell
17	chr12:56752800-56754000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
18	chr12:56752800-56754600	Active TSS	HepG2	liver
19	chr12:56752800-56754800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr12:56752800-56754800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr12:56752800-56754800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr12:56752800-56754800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr12:56752800-56754800	Active TSS	Colonic Mucosa	Colon
24	chr12:56752800-56754800	Active TSS	Lung	lung
25	chr12:56752800-56754800	Active TSS	Ovary	ovary
26	chr12:56752800-56754800	Active TSS	Right Atrium	heart
27	chr12:56752800-56754800	Active TSS	NHLF	lung
28	chr12:56752800-56755000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr12:56752800-56755000	Active TSS	Brain Inferior Temporal Lobe	brain
30	chr12:56752800-56755000	Active TSS	Fetal Kidney	kidney
31	chr12:56752800-56755000	Active TSS	Psoas Muscle	Psoas
32	chr12:56752800-56755000	Active TSS	HSMM	muscle
33	chr12:56752800-56755000	Active TSS	NHDF-Ad	bronchial
34	chr12:56752800-56755200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr12:56753000-56754600	Active TSS	Small Intestine	intestine
36	chr12:56753000-56754800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr12:56753000-56754800	Active TSS	iPS-15b Cell Line	embryonic stem cell
38	chr12:56753000-56754800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr12:56753000-56754800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
40	chr12:56753000-56754800	Active TSS	Pancreatic Islets	Pancreatic Islet
41	chr12:56753000-56754800	Active TSS	K562	blood
42	chr12:56753000-56755000	Active TSS	H1 Cell Line	embryonic stem cell
43	chr12:56753000-56755000	Active TSS	H9 Cell Line	embryonic stem cell
44	chr12:56753000-56755600	Active TSS	Brain Anterior Caudate	brain
45	chr12:56753200-56754400	Active TSS	Primary monocytes fromperipheralblood	blood
46	chr12:56753200-56754400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
47	chr12:56753200-56754400	Active TSS	Fetal Thymus	thymus
48	chr12:56753200-56754600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr12:56753200-56754600	Active TSS	Primary T cells fromperipheralblood	blood
50	chr12:56753200-56754600	Active TSS	Primary T helper cells PMA-I stimulated	--

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