Variant report

Variant	rs3742061
Chromosome Location	chr12:46763770-46763771
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	chr12:46750625-46766899	K562	blood:	n/a	n/a
2	POLR2A	chr12:46756521-46767732	H1-hESC	embryonic stem cell:	n/a	n/a
3	FOXA1	chr12:46763588-46763961	HepG2	liver:	n/a	chr12:46763732-46763744 chr12:46763819-46763834
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	FOXA1	chr12:46763549-46763977	HepG2	liver:	n/a	chr12:46763732-46763744 chr12:46763819-46763834
11	POLR2A	chr12:46758662-46766869	HUVEC	blood vessel:	n/a	n/a
12	CHD1	chr12:46763609-46766632	H1-hESC	embryonic stem cell:	n/a	chr12:46765445-46765455 chr12:46766470-46766477
13	CHD1	chr12:46756240-46768821	IMR90	lung:	n/a	chr12:46765445-46765455 chr12:46766470-46766477 chr12:46768496-46768506 chr12:46768499-46768509
14	NFIC	chr12:46762484-46764067	HepG2	liver:	n/a	n/a
15	POLR2A	chr12:46754387-46768013	PANC-1	pancreas:	n/a	n/a
16	MYC	chr12:46763732-46763896	MCF10A-Er-Src	breast:	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	ARID3A	chr12:46763723-46763965	HepG2	liver:	n/a	n/a
25	FOXA1	chr12:46763643-46763950	T-47D	breast:	n/a	chr12:46763732-46763744 chr12:46763819-46763834
26	POLR2A	chr12:46761002-46763912	GM12878	blood:	n/a	n/a
27	POLR2A	chr12:46758139-46766914	MCF-7	breast:	n/a	n/a
28	POLR2A	chr12:46754358-46767861	HepG2	liver:	n/a	n/a
29	MXI1	chr12:46763642-46767716	SK-N-SH	brain:	n/a	chr12:46765211-46765220
30	POLR2A	chr12:46755082-46767953	HCT-116	colon:	n/a	n/a
31	POLR2A	chr12:46758424-46767361	MCF10A-Er-Src	breast:	n/a	n/a
32	CEBPB	chr12:46763207-46763773	IMR90	lung:	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	HEY1	chr12:46750801-46768173	HepG2	liver:	n/a	chr12:46766614-46766629 chr12:46766074-46766089 chr12:46765229-46765244
36	POLR2A	chr12:46762399-46766943	HUVEC	blood vessel:	n/a	n/a
37	POLR2A	chr12:46761038-46764152	ProgFib	skin:	n/a	n/a
38	MBD4	chr12:46750663-46767066	HepG2	liver:	n/a	n/a
39	FOXA1	chr12:46763483-46764013	HepG2	liver:	n/a	chr12:46763732-46763744 chr12:46763819-46763834
40	POLR2A	chr12:46761151-46764466	GM12891	blood:	n/a	n/a
41	FOXA2	chr12:46763570-46763985	HepG2	liver:	n/a	chr12:46763732-46763744
42	POLR2A	chr12:46760588-46763976	K562	blood:	n/a	n/a
43	POLR2A	chr12:46760978-46764013	GM12878	blood:	n/a	n/a
44	POLR2A	chr12:46754307-46767479	SK-N-SH	brain:	n/a	n/a
45	POLR2A	chr12:46750204-46767088	U87	brain:	n/a	n/a
46	POLR2A	chr12:46763759-46764016	H1-hESC	embryonic stem cell:	n/a	n/a
47	POLR2A	chr12:46758610-46767931	HUVEC	blood vessel:	n/a	n/a
48	POLR2A	chr12:46763674-46763970	H1-hESC	embryonic stem cell:	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.	Distal block	Cell Line	Cell type
1	chr12:46656458..46664971-chr12:46763618..46767965,19	MCF-7	breast:
2	chr12:46652597..46666608-chr12:46757245..46767985,36	MCF-7	breast:
3	chr12:46762092..46763776-chr12:46876026..46877970,3	K562	blood:
4	chr12:46381030..46386260-chr12:46762457..46768592,6	K562	blood:
5	chr12:46383804..46386112-chr12:46763445..46766511,3	MCF-7	breast:
6	chr12:46761697..46764452-chr12:46853963..46855507,2	MCF-7	breast:
7	chr12:46119720..46123062-chr12:46761797..46766025,4	K562	blood:
8	chr12:46119720..46122632-chr12:46763272..46766407,3	K562	blood:
9	chr12:46381426..46387093-chr12:46763754..46767064,8	MCF-7	breast:
10	chr12:46762091..46764128-chr12:47051293..47053503,2	K562	blood:
11	chr12:46659532..46664131-chr12:46762494..46766775,7	K562	blood:
12	chr12:46762605..46765177-chr19:38791168..38793279,2	MCF-7	breast:
13	chr12:46658047..46664131-chr12:46762494..46767686,10	K562	blood:
14	chr12:46382586..46387481-chr12:46763277..46769922,9	K562	blood:
15	chr12:46762602..46765130-chr12:46800260..46802192,2	K562	blood:
16	chr12:46516152..46518764-chr12:46762131..46764765,2	MCF-7	breast:

Variant related genes	Relation type
SLC38A2	TF binding region
ENSG00000258096	TF binding region
ENSG00000273015	Chromatin interaction
ENSG00000111371	Chromatin interaction
ENSG00000139218	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10467215	0.83[CHB][hapmap]
rs10506267	0.84[CHB][hapmap];1.00[EUR][1000 genomes]
rs10506268	1.00[EUR][1000 genomes]
rs11183454	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11183467	0.88[CHB][hapmap];0.83[JPT][hapmap];1.00[AMR][1000 genomes]
rs11183482	0.88[CHB][hapmap];0.83[JPT][hapmap];1.00[AMR][1000 genomes]
rs11183487	1.00[AMR][1000 genomes]
rs11183500	0.83[CHB][hapmap]
rs11183510	0.82[CHB][hapmap]
rs1125908	1.00[CHB][hapmap];0.94[JPT][hapmap];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	0.85[CHB][hapmap];1.00[AMR][1000 genomes]
rs12317255	0.88[CHB][hapmap];0.83[JPT][hapmap];1.00[AMR][1000 genomes]
rs12320438	1.00[AMR][1000 genomes]
rs12321512	0.94[CHB][hapmap];0.84[JPT][hapmap]
rs12321642	1.00[AMR][1000 genomes]
rs12321960	0.83[CHB][hapmap]
rs12322378	1.00[AMR][1000 genomes]
rs13377959	0.88[CHB][hapmap];1.00[AMR][1000 genomes]
rs17096884	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17096896	0.94[CHB][hapmap];0.84[JPT][hapmap];1.00[AMR][1000 genomes]
rs17096922	0.88[CHB][hapmap];0.84[JPT][hapmap];1.00[AMR][1000 genomes]
rs1948425	0.89[JPT][hapmap]
rs2125646	0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[EUR][1000 genomes]
rs2307059	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs2307062	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2307063	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2408509	0.94[CHB][hapmap];0.94[JPT][hapmap];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]
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	0.93[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]
rs61406609	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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]
rs7953339	0.82[CHB][hapmap]
rs7954314	0.88[CHB][hapmap];0.83[JPT][hapmap];1.00[AMR][1000 genomes]
rs7965618	1.00[AMR][1000 genomes]
rs7967889	0.89[CHB][hapmap];0.84[JPT][hapmap];1.00[AMR][1000 genomes]
rs7977319	1.00[AMR][1000 genomes]
rs7980023	0.82[CHB][hapmap]
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	chr12:46752600-46764200	Strong transcription	Fetal Muscle Trunk	muscle
4	chr12:46753400-46764200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr12:46753600-46765200	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr12:46754000-46765800	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr12:46754600-46765000	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
8	chr12:46755400-46766000	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr12:46756600-46765200	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr12:46756800-46766000	Transcr. at gene 5' and 3'	NHLF	lung
11	chr12:46757400-46766000	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
12	chr12:46758400-46765200	Transcr. at gene 5' and 3'	HUVEC	blood vessel
13	chr12:46758600-46765000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr12:46758800-46763800	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr12:46758800-46763800	Genic enhancers	Fetal Intestine Large	intestine
16	chr12:46758800-46765600	Transcr. at gene 5' and 3'	A549	lung
17	chr12:46758800-46765600	Transcr. at gene 5' and 3'	Osteobl	bone
18	chr12:46758800-46766000	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr12:46758800-46766000	Transcr. at gene 5' and 3'	NHEK	skin
20	chr12:46759000-46764400	Transcr. at gene 5' and 3'	HepG2	liver
21	chr12:46759600-46764400	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr12:46759600-46765000	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr12:46759600-46765000	Transcr. at gene 5' and 3'	NH-A	brain
24	chr12:46759600-46765200	Transcr. at gene 5' and 3'	Hela-S3	cervix
25	chr12:46759600-46765200	Transcr. at gene 5' and 3'	HMEC	breast
26	chr12:46759800-46764400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr12:46760000-46764000	Genic enhancers	Primary monocytes fromperipheralblood	blood
28	chr12:46760200-46765200	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
29	chr12:46760400-46766200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr12:46760600-46763800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr12:46760600-46766000	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr12:46760600-46766000	Transcr. at gene 5' and 3'	Dnd41	blood
33	chr12:46760800-46765000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr12:46761000-46763800	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
35	chr12:46761000-46764400	Genic enhancers	Cortex derived primary cultured neurospheres	brain
36	chr12:46761000-46764600	Transcr. at gene 5' and 3'	Brain Anterior Caudate	brain
37	chr12:46761200-46763800	Transcr. at gene 5' and 3'	Brain Dorsolateral Prefrontal Cortex	brain
38	chr12:46761200-46764000	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
39	chr12:46761200-46764400	Transcr. at gene 5' and 3'	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr12:46761200-46764400	Transcr. at gene 5' and 3'	Brain Inferior Temporal Lobe	brain
41	chr12:46761200-46764400	Transcr. at gene 5' and 3'	Duodenum Mucosa	Duodenum
42	chr12:46761200-46764400	Transcr. at gene 5' and 3'	Left Ventricle	heart
43	chr12:46761200-46764400	Transcr. at gene 5' and 3'	HSMMtube	muscle
44	chr12:46761200-46764600	Genic enhancers	Primary B cells from peripheral blood	blood
45	chr12:46761200-46764800	Transcr. at gene 5' and 3'	Brain Hippocampus Middle	brain
46	chr12:46761200-46765000	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr12:46761200-46765000	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 29	rectum
48	chr12:46761200-46765000	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
49	chr12:46761200-46765200	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
50	chr12:46761200-46765200	Transcr. at gene 5' and 3'	Adipose Nuclei	Adipose

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