Variant report

Variant	rs61406609
Chromosome Location	chr12:46763281-46763282
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:86)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:86 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:46750625-46766899	K562	blood:	n/a	n/a
2	REST	chr12:46763036-46763382	HepG2	liver:	n/a	n/a
3	POLR2A	chr12:46756521-46767732	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr12:46750469-46766708	HepG2	liver:	n/a	n/a
5	POLR2A	chr12:46760573-46767926	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr12:46750482-46767845	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr12:46760857-46764495	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr12:46754517-46767857	HepG2	liver:	n/a	n/a
9	POLR2A	chr12:46750751-46768006	HepG2	liver:	n/a	n/a
10	POLR2A	chr12:46758662-46766869	HUVEC	blood vessel:	n/a	n/a
11	CHD1	chr12:46756240-46768821	IMR90	lung:	n/a	chr12:46765445-46765455 chr12:46766470-46766477 chr12:46768496-46768506 chr12:46768499-46768509
12	NFIC	chr12:46762484-46764067	HepG2	liver:	n/a	n/a
13	POLR2A	chr12:46762796-46763360	GM12891	blood:	n/a	n/a
14	CEBPB	chr12:46762737-46763536	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr12:46754387-46768013	PANC-1	pancreas:	n/a	n/a
16	POLR2A	chr12:46762841-46763736	K562	blood:	n/a	n/a
17	SMC3	chr12:46763256-46764054	HepG2	liver:	n/a	n/a
18	POLR2A	chr12:46754499-46767455	HUVEC	blood vessel:	n/a	n/a
19	POLR2A	chr12:46757607-46767342	MCF10A-Er-Src	breast:	n/a	n/a
20	POLR2A	chr12:46760364-46767099	SK-N-MC	brain:	n/a	n/a
21	POLR2A	chr12:46750487-46766675	A549	lung:	n/a	n/a
22	POLR2A	chr12:46758684-46767978	Hela-S3	cervix:	n/a	n/a
23	CEBPB	chr12:46763179-46763846	A549	lung:	n/a	n/a
24	POLR2A	chr12:46762845-46763333	GM12891	blood:	n/a	n/a
25	POLR2A	chr12:46761002-46763912	GM12878	blood:	n/a	n/a
26	POLR2A	chr12:46758139-46766914	MCF-7	breast:	n/a	n/a
27	POLR2A	chr12:46754358-46767861	HepG2	liver:	n/a	n/a
28	POLR2A	chr12:46763167-46763557	K562	blood:	n/a	n/a
29	POLR2A	chr12:46755082-46767953	HCT-116	colon:	n/a	n/a
30	POLR2A	chr12:46758424-46767361	MCF10A-Er-Src	breast:	n/a	n/a
31	CEBPB	chr12:46763207-46763773	IMR90	lung:	n/a	n/a
32	TBL1XR1	chr12:46762833-46763546	K562	blood:	n/a	n/a
33	POLR2A	chr12:46750385-46767599	IMR90	lung:	n/a	n/a
34	HEY1	chr12:46762768-46763886	HepG2	liver:	n/a	n/a
35	POLR2A	chr12:46763235-46763726	GM12892	blood:	n/a	n/a
36	HEY1	chr12:46750801-46768173	HepG2	liver:	n/a	chr12:46766614-46766629 chr12:46766074-46766089 chr12:46765229-46765244
37	ELK4	chr12:46762624-46763307	Hela-S3	cervix:	n/a	n/a
38	POLR2A	chr12:46762399-46766943	HUVEC	blood vessel:	n/a	n/a
39	POLR2A	chr12:46761038-46764152	ProgFib	skin:	n/a	n/a
40	MBD4	chr12:46750663-46767066	HepG2	liver:	n/a	n/a
41	POLR2A	chr12:46762853-46763545	GM12892	blood:	n/a	n/a
42	POLR2A	chr12:46761151-46764466	GM12891	blood:	n/a	n/a
43	POLR2A	chr12:46760588-46763976	K562	blood:	n/a	n/a
44	POLR2A	chr12:46762993-46763647	GM12891	blood:	n/a	n/a
45	POLR2A	chr12:46760978-46764013	GM12878	blood:	n/a	n/a
46	POLR2A	chr12:46754307-46767479	SK-N-SH	brain:	n/a	n/a
47	POLR2A	chr12:46750204-46767088	U87	brain:	n/a	n/a
48	POLR2A	chr12:46758610-46767931	HUVEC	blood vessel:	n/a	n/a
49	POLR2A	chr12:46759062-46767808	Hela-S3	cervix:	n/a	n/a
50	POLR2A	chr12:46760481-46767380	U87	brain:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr12:46652597..46666608-chr12:46757245..46767985,36	MCF-7	breast:
2	chr12:46762092..46763776-chr12:46876026..46877970,3	K562	blood:
3	chr12:46381030..46386260-chr12:46762457..46768592,6	K562	blood:
4	chr12:46761697..46764452-chr12:46853963..46855507,2	MCF-7	breast:
5	chr12:46119720..46123062-chr12:46761797..46766025,4	K562	blood:
6	chr12:46119720..46122632-chr12:46763272..46766407,3	K562	blood:
7	chr12:46762091..46764128-chr12:47051293..47053503,2	K562	blood:
8	chr12:46542942..46545792-chr12:46762103..46763694,2	MCF-7	breast:
9	chr12:46659532..46664131-chr12:46762494..46766775,7	K562	blood:
10	chr12:46761905..46763555-chr15:56533896..56536634,2	MCF-7	breast:
11	chr12:46762605..46765177-chr19:38791168..38793279,2	MCF-7	breast:
12	chr12:46658047..46664131-chr12:46762494..46767686,10	K562	blood:
13	chr12:46382586..46387481-chr12:46763277..46769922,9	K562	blood:
14	chr12:46761485..46763714-chr12:46828699..46831336,2	MCF-7	breast:
15	chr12:46672529..46674114-chr12:46761613..46763719,2	MCF-7	breast:
16	chr12:46762602..46765130-chr12:46800260..46802192,2	K562	blood:
17	chr12:46516152..46518764-chr12:46762131..46764765,2	MCF-7	breast:
18	chr12:46762786..46763334-chr9:114393145..114393657,2	HCT-116	colon:

No data

Variant related genes	Relation type
ENSG00000258096	TF binding region
SLC38A2	TF binding region
ENSG00000151575	Chromatin interaction
ENSG00000204173	Chromatin interaction
ENSG00000111371	Chromatin interaction
ENSG00000139218	Chromatin interaction
ENSG00000273015	Chromatin interaction
ENSG00000059769	Chromatin interaction
ENSG00000181827	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10506267	1.00[EUR][1000 genomes]
rs10506268	1.00[EUR][1000 genomes]
rs11183454	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11183467	1.00[AMR][1000 genomes]
rs11183482	1.00[AMR][1000 genomes]
rs11183487	1.00[AMR][1000 genomes]
rs1125908	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11830769	1.00[EUR][1000 genomes]
rs11834593	0.85[ASN][1000 genomes]
rs11834905	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12299499	1.00[AMR][1000 genomes]
rs12317255	1.00[AMR][1000 genomes]
rs12320438	1.00[AMR][1000 genomes]
rs12321642	1.00[AMR][1000 genomes]
rs12322378	1.00[AMR][1000 genomes]
rs13377959	1.00[AMR][1000 genomes]
rs17096884	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17096896	1.00[AMR][1000 genomes]
rs17096922	1.00[AMR][1000 genomes]
rs2125646	1.00[EUR][1000 genomes]
rs2307062	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2307063	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2408509	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34280632	1.00[AMR][1000 genomes]
rs35875247	1.00[AMR][1000 genomes]
rs36010856	1.00[AMR][1000 genomes]
rs3742061	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55795804	0.81[ASN][1000 genomes]
rs56036156	1.00[AMR][1000 genomes]
rs56196954	1.00[AMR][1000 genomes]
rs56222195	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56314009	1.00[AMR][1000 genomes]
rs57067899	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57149475	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57271454	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57425661	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58460251	1.00[AMR][1000 genomes]
rs58890669	1.00[AMR][1000 genomes]
rs59608605	1.00[AMR][1000 genomes]
rs60565802	1.00[AMR][1000 genomes]
rs60628240	1.00[EUR][1000 genomes]
rs60878594	1.00[AMR][1000 genomes]
rs60977966	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61232019	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61517444	1.00[EUR][1000 genomes]
rs73282532	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73282561	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73282591	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73290315	1.00[AMR][1000 genomes]
rs74082254	1.00[AMR][1000 genomes]
rs74083707	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs74083710	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs74084031	1.00[EUR][1000 genomes]
rs7488027	1.00[AMR][1000 genomes]
rs7954314	1.00[AMR][1000 genomes]
rs7965618	1.00[AMR][1000 genomes]
rs7967889	1.00[AMR][1000 genomes]
rs7977319	1.00[AMR][1000 genomes]
rs923788	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832398	chr12:46611692-46825530	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	esv1842882	chr12:46691487-47009428	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
3	nsv1049525	chr12:46721742-47264172	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
4	nsv541486	chr12:46721742-47264172	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
5	esv3429861	chr12:46762813-46988789	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	145 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46748800-46764200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:46752400-46764200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr12:46752600-46763600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:46752600-46764200	Strong transcription	Fetal Muscle Trunk	muscle
5	chr12:46753400-46764200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr12:46753600-46765200	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr12:46754000-46765800	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr12:46754600-46765000	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
9	chr12:46755400-46766000	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr12:46756600-46765200	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr12:46756800-46766000	Transcr. at gene 5' and 3'	NHLF	lung
12	chr12:46757000-46763600	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr12:46757400-46766000	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
14	chr12:46758400-46765200	Transcr. at gene 5' and 3'	HUVEC	blood vessel
15	chr12:46758600-46765000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr12:46758800-46763800	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr12:46758800-46763800	Genic enhancers	Fetal Intestine Large	intestine
18	chr12:46758800-46765600	Transcr. at gene 5' and 3'	A549	lung
19	chr12:46758800-46765600	Transcr. at gene 5' and 3'	Osteobl	bone
20	chr12:46758800-46766000	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr12:46758800-46766000	Transcr. at gene 5' and 3'	NHEK	skin
22	chr12:46759000-46764400	Transcr. at gene 5' and 3'	HepG2	liver
23	chr12:46759600-46764400	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr12:46759600-46765000	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr12:46759600-46765000	Transcr. at gene 5' and 3'	NH-A	brain
26	chr12:46759600-46765200	Transcr. at gene 5' and 3'	Hela-S3	cervix
27	chr12:46759600-46765200	Transcr. at gene 5' and 3'	HMEC	breast
28	chr12:46759800-46764400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr12:46760000-46764000	Genic enhancers	Primary monocytes fromperipheralblood	blood
30	chr12:46760200-46765200	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
31	chr12:46760400-46766200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr12:46760600-46763800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
33	chr12:46760600-46766000	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr12:46760600-46766000	Transcr. at gene 5' and 3'	Dnd41	blood
35	chr12:46760800-46765000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr12:46761000-46763800	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
37	chr12:46761000-46764400	Genic enhancers	Cortex derived primary cultured neurospheres	brain
38	chr12:46761000-46764600	Transcr. at gene 5' and 3'	Brain Anterior Caudate	brain
39	chr12:46761200-46763400	Transcr. at gene 5' and 3'	Aorta	Aorta
40	chr12:46761200-46763400	Genic enhancers	Fetal Muscle Leg	muscle
41	chr12:46761200-46763600	Genic enhancers	Placenta	Placenta
42	chr12:46761200-46763800	Transcr. at gene 5' and 3'	Brain Dorsolateral Prefrontal Cortex	brain
43	chr12:46761200-46764000	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
44	chr12:46761200-46764400	Transcr. at gene 5' and 3'	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr12:46761200-46764400	Transcr. at gene 5' and 3'	Brain Inferior Temporal Lobe	brain
46	chr12:46761200-46764400	Transcr. at gene 5' and 3'	Duodenum Mucosa	Duodenum
47	chr12:46761200-46764400	Transcr. at gene 5' and 3'	Left Ventricle	heart
48	chr12:46761200-46764400	Transcr. at gene 5' and 3'	HSMMtube	muscle
49	chr12:46761200-46764600	Genic enhancers	Primary B cells from peripheral blood	blood
50	chr12:46761200-46764800	Transcr. at gene 5' and 3'	Brain Hippocampus Middle	brain

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