Variant report

Variant	rs730566
Chromosome Location	chr3:48487048-48487049
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:37)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:37 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:48486778-48487136	GM12878	blood:	n/a	n/a
2	POLR2A	chr3:48486757-48487062	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr3:48486671-48487101	ECC-1	luminal epithelium:	n/a	n/a
4	POLR2A	chr3:48485860-48488666	GM12891	blood:	n/a	n/a
5	POLR2A	chr3:48485350-48488730	PFSK-1	brain:	n/a	n/a
6	POLR2A	chr3:48486507-48487435	PANC-1	pancreas:	n/a	n/a
7	POLR2A	chr3:48485828-48487191	U87	brain:	n/a	n/a
8	POLR2A	chr3:48485975-48487498	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr3:48486660-48488714	GM12892	blood:	n/a	n/a
10	POLR2A	chr3:48485869-48487078	PANC-1	pancreas:	n/a	n/a
11	POLR2A	chr3:48486692-48487265	U87	brain:	n/a	n/a
12	POLR2A	chr3:48485860-48487052	HUVEC	blood vessel:	n/a	n/a
13	MTA3	chr3:48485674-48488326	GM12878	blood:	n/a	n/a
14	POLR2A	chr3:48485480-48488528	SK-N-MC	brain:	n/a	n/a
15	POLR2A	chr3:48485793-48487443	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr3:48485560-48487612	PFSK-1	brain:	n/a	n/a
17	POLR2A	chr3:48485869-48488641	SK-N-SH	brain:	n/a	n/a
18	POLR2A	chr3:48485898-48488594	GM12878	blood:	n/a	n/a
19	POLR2A	chr3:48485436-48488575	GM12892	blood:	n/a	n/a
20	POLR2A	chr3:48486668-48487265	U87	brain:	n/a	n/a
21	POLR2A	chr3:48485870-48488879	K562	blood:	n/a	n/a
22	POLR2A	chr3:48485493-48489452	HepG2	liver:	n/a	n/a
23	POLR2A	chr3:48486550-48487119	GM12878	blood:	n/a	n/a
24	NFATC1	chr3:48486686-48487071	GM12878	blood:	n/a	n/a
25	POLR2A	chr3:48485778-48488613	GM12891	blood:	n/a	n/a
26	POLR2A	chr3:48486588-48488643	GM12892	blood:	n/a	n/a
27	POLR2A	chr3:48486647-48488468	GM12891	blood:	n/a	n/a
28	POLR2A	chr3:48486741-48487091	GM12892	blood:	n/a	n/a
29	POLR2A	chr3:48486518-48487072	HUVEC	blood vessel:	n/a	n/a
30	POLR2A	chr3:48485586-48487509	K562	blood:	n/a	n/a
31	POLR2A	chr3:48485446-48488566	GM12878	blood:	n/a	n/a
32	MTA3	chr3:48486749-48487108	GM12878	blood:	n/a	n/a
33	POLR2A	chr3:48485914-48488417	GM12878	blood:	n/a	n/a
34	POLR2A	chr3:48486583-48487311	MCF-7	breast:	n/a	n/a
35	POLR2A	chr3:48485851-48488721	HUVEC	blood vessel:	n/a	n/a
36	POLR2A	chr3:48485794-48487197	U87	brain:	n/a	n/a
37	POLR2A	chr3:48485947-48488432	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:48469445..48473059-chr3:48486174..48489531,5	MCF-7	breast:
2	chr15:42263480..42264426-chr3:48486566..48487176,2	NB4	blood:
3	chr3:48485232..48487898-chr3:48541366..48542951,2	K562	blood:
4	chr3:48460976..48462671-chr3:48486369..48489165,2	MCF-7	breast:
5	chr3:48477555..48484761-chr3:48484855..48490000,13	MCF-7	breast:
6	chr3:48468360..48471756-chr3:48485148..48489754,5	K562	blood:
7	chr3:48486835..48489928-chr3:48540255..48543800,6	MCF-7	breast:
8	chr3:48486334..48488063-chr3:48594171..48595954,2	MCF-7	breast:
9	chr3:48486933..48489526-chr3:48585390..48587565,2	MCF-7	breast:
10	chr3:48485967..48488247-chr3:48600373..48602900,2	MCF-7	breast:
11	chr3:48486214..48489756-chr3:48493754..48497547,4	K562	blood:
12	chr3:48484123..48488497-chr3:48591865..48597132,6	K562	blood:
13	chr3:48485548..48495296-chr3:48503776..48510303,13	MCF-7	breast:
14	chr3:48341768..48344382-chr3:48487005..48489358,2	K562	blood:
15	chr3:48486535..48489941-chr3:48491977..48496128,7	MCF-7	breast:
16	chr3:48341910..48343501-chr3:48486949..48488485,2	MCF-7	breast:
17	chr3:48228273..48230987-chr3:48484727..48487110,2	K562	blood:
18	chr3:48487008..48490928-chr3:48507402..48510491,5	K562	blood:

No data

Variant related genes	Relation type
ATRIP	TF binding region
ENSG00000145040	Chromatin interaction
ENSG00000164051	Chromatin interaction
ENSG00000213689	Chromatin interaction
ENSG00000164045	Chromatin interaction
ENSG00000114268	Chromatin interaction
ENSG00000232112	Chromatin interaction
ENSG00000114270	Chromatin interaction
ENSG00000164054	Chromatin interaction
ENSG00000164050	Chromatin interaction
ENSG00000164053	Chromatin interaction
ENSG00000172113	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1037773	0.90[JPT][hapmap]
rs10470686	0.82[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap]
rs1109227	0.90[JPT][hapmap]
rs11130170	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs11130171	0.83[CHD][hapmap];0.90[JPT][hapmap]
rs11797	0.81[CHD][hapmap];0.85[JPT][hapmap]
rs1264194	0.82[ASW][hapmap];0.81[JPT][hapmap]
rs13076076	0.83[CHD][hapmap];0.90[JPT][hapmap]
rs13314659	0.82[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap]
rs1459242	0.82[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap]
rs1563736	0.82[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap]
rs2242150	0.81[CHD][hapmap];0.90[JPT][hapmap]
rs2267846	0.82[ASW][hapmap]
rs2279077	0.83[CHD][hapmap];0.90[JPT][hapmap]
rs2290822	0.83[CHD][hapmap];0.90[JPT][hapmap]
rs2362450	0.90[JPT][hapmap]
rs2362452	0.82[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap]
rs2885510	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs3214041	0.82[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap]
rs3774808	0.83[CHD][hapmap];0.90[JPT][hapmap]
rs4858795	0.81[CHD][hapmap];0.85[JPT][hapmap]
rs4858819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4858820	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56298324	0.84[ASN][1000 genomes]
rs6442117	0.83[CHD][hapmap];0.95[JPT][hapmap]
rs6442118	0.82[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap]
rs6442119	0.82[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap]
rs6442120	0.83[CHD][hapmap];0.90[JPT][hapmap]
rs6776700	0.83[CHD][hapmap];0.90[JPT][hapmap]
rs6794875	0.83[CHD][hapmap];0.90[JPT][hapmap]
rs725309	0.80[CHB][hapmap];0.95[JPT][hapmap]
rs725310	0.82[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap]
rs734071	0.81[CHD][hapmap];0.85[JPT][hapmap]
rs7636044	0.90[JPT][hapmap]
rs7651407	0.82[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap]
rs898225	0.82[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap]
rs922075	0.81[CHD][hapmap];0.90[JPT][hapmap]
rs9311428	0.81[CHD][hapmap];0.85[JPT][hapmap]
rs9812647	0.82[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap]
rs9815103	0.82[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap]
rs9838618	0.83[CHD][hapmap];0.90[JPT][hapmap]
rs9849509	0.83[CHD][hapmap];0.90[JPT][hapmap]
rs9876781	0.83[CHD][hapmap];0.90[JPT][hapmap]
rs9883759	0.90[JPT][hapmap]
rs9883927	0.83[CHD][hapmap];0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834683	chr3:48301504-48493261	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	nsv834684	chr3:48385699-48589323	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv590242	chr3:48433635-48556339	Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
4	nsv876761	chr3:48464968-48496758	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Prion diseases	22210626	GWAS catalog

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs730566	IQCF1	cis	cerebellum	SCAN
rs730566	DALRD3	cis	parietal	SCAN
rs730566	QRICH1	cis	cerebellum	SCAN
rs730566	WDR6	cis	multi-tissue	Pritchard
rs730566	AMT	cis	Thyroid	GTEx
rs730566	CCDC12	cis	cerebellum	SCAN
rs730566	ATRIP	cis	cerebellum	SCAN
rs730566	TMA7	cis	Muscle Skeletal	GTEx
rs730566	PLXNB1	cis	lymphoblastoid	seeQTL
rs730566	TMIE	cis	cerebellum	SCAN
rs730566	WDR6	cis	cerebellum	SCAN
rs730566	P4HTM	cis	parietal	SCAN
rs730566	TREX1	Cis_1M	lymphoblastoid	RTeQTL
rs730566	ZNF589	cis	parietal	SCAN
rs730566	AMT	cis	parietal	SCAN
rs730566	ZNF589	cis	cerebellum	SCAN
rs730566	NCKIPSD	cis	multi-tissue	Pritchard
rs730566	NICN1	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48482600-48487200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:48482600-48487200	Weak transcription	Right Atrium	heart
3	chr3:48482600-48487400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:48482600-48487600	Weak transcription	Ovary	ovary
5	chr3:48483200-48487200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr3:48483400-48487200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr3:48483400-48487200	Weak transcription	Brain Angular Gyrus	brain
8	chr3:48483400-48487400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr3:48483400-48487600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr3:48483600-48487200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr3:48483600-48487200	Weak transcription	Fetal Brain Male	brain
12	chr3:48483600-48487200	Strong transcription	Fetal Muscle Leg	muscle
13	chr3:48483600-48487200	Strong transcription	Fetal Stomach	stomach
14	chr3:48483600-48487400	Weak transcription	Psoas Muscle	Psoas
15	chr3:48483600-48487400	Weak transcription	Stomach Mucosa	stomach
16	chr3:48483800-48487200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr3:48483800-48487200	Weak transcription	Small Intestine	intestine
18	chr3:48483800-48487400	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr3:48484400-48487200	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr3:48484400-48487200	Weak transcription	K562	blood
21	chr3:48484600-48487200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr3:48484600-48487200	Weak transcription	Colonic Mucosa	Colon
23	chr3:48484800-48487200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr3:48484800-48487400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr3:48485000-48487200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr3:48485200-48487200	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr3:48485200-48487200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr3:48485200-48487200	Weak transcription	Fetal Lung	lung
29	chr3:48485200-48487200	Weak transcription	HSMMtube	muscle
30	chr3:48485200-48487400	Weak transcription	Right Ventricle	heart
31	chr3:48485800-48487200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr3:48485800-48487200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr3:48485800-48487200	Weak transcription	HSMM	muscle
34	chr3:48486000-48487200	Weak transcription	Primary hematopoietic stem cells	blood
35	chr3:48486000-48487200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr3:48486000-48487200	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr3:48486000-48487200	Weak transcription	Fetal Intestine Large	intestine
38	chr3:48486000-48487400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr3:48486200-48487200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr3:48486200-48487200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr3:48486200-48487200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr3:48486200-48487200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr3:48486200-48487200	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr3:48486200-48487200	Weak transcription	Liver	Liver
45	chr3:48486200-48487200	Weak transcription	Fetal Kidney	kidney
46	chr3:48486200-48487200	Weak transcription	Fetal Thymus	thymus
47	chr3:48486200-48487200	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr3:48486200-48487200	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr3:48486200-48487200	Weak transcription	Osteobl	bone
50	chr3:48486200-48487400	Weak transcription	Lung	lung

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