Variant report

Variant	rs56222195
Chromosome Location	chr12:46761916-46761917
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:77)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:77 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:46761895-46762258	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr12:46750625-46766899	K562	blood:	n/a	n/a
3	POLR2A	chr12:46761908-46762250	GM12891	blood:	n/a	n/a
4	POLR2A	chr12:46756521-46767732	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr12:46760562-46762281	HepG2	liver:	n/a	n/a
6	POLR2A	chr12:46750469-46766708	HepG2	liver:	n/a	n/a
7	POLR2A	chr12:46760573-46767926	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr12:46761819-46762191	GM12892	blood:	n/a	n/a
9	POLR2A	chr12:46750482-46767845	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr12:46760857-46764495	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr12:46754517-46767857	HepG2	liver:	n/a	n/a
12	POLR2A	chr12:46750751-46768006	HepG2	liver:	n/a	n/a
13	POLR2A	chr12:46761827-46762337	PFSK-1	brain:	n/a	n/a
14	POLR2A	chr12:46758662-46766869	HUVEC	blood vessel:	n/a	n/a
15	POLR2A	chr12:46761168-46762238	K562	blood:	n/a	n/a
16	CHD1	chr12:46756240-46768821	IMR90	lung:	n/a	chr12:46765445-46765455 chr12:46766470-46766477 chr12:46768496-46768506 chr12:46768499-46768509
17	POLR2A	chr12:46761147-46762062	GM12891	blood:	n/a	n/a
18	POLR2A	chr12:46754387-46768013	PANC-1	pancreas:	n/a	n/a
19	WRNIP1	chr12:46761253-46762200	GM12878	blood:	n/a	n/a
20	POLR2A	chr12:46761019-46762624	GM12892	blood:	n/a	n/a
21	POLR2A	chr12:46754499-46767455	HUVEC	blood vessel:	n/a	n/a
22	JUND	chr12:46761593-46762741	SK-N-SH	brain:	n/a	n/a
23	POLR2A	chr12:46760417-46762116	HUVEC	blood vessel:	n/a	n/a
24	HEY1	chr12:46761862-46762265	HepG2	liver:	n/a	n/a
25	HEY1	chr12:46761189-46762193	K562	blood:	n/a	n/a
26	POLR2A	chr12:46757607-46767342	MCF10A-Er-Src	breast:	n/a	n/a
27	POLR2A	chr12:46760364-46767099	SK-N-MC	brain:	n/a	n/a
28	POLR2A	chr12:46750487-46766675	A549	lung:	n/a	n/a
29	POLR2A	chr12:46758684-46767978	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr12:46761002-46763912	GM12878	blood:	n/a	n/a
31	POLR2A	chr12:46758139-46766914	MCF-7	breast:	n/a	n/a
32	POLR2A	chr12:46754358-46767861	HepG2	liver:	n/a	n/a
33	POLR2A	chr12:46761156-46762549	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr12:46755082-46767953	HCT-116	colon:	n/a	n/a
35	NFIC	chr12:46761603-46762367	HepG2	liver:	n/a	n/a
36	POLR2A	chr12:46758424-46767361	MCF10A-Er-Src	breast:	n/a	n/a
37	POLR2A	chr12:46750385-46767599	IMR90	lung:	n/a	n/a
38	POLR2A	chr12:46760980-46762251	GM12891	blood:	n/a	n/a
39	HEY1	chr12:46750801-46768173	HepG2	liver:	n/a	chr12:46766614-46766629 chr12:46766074-46766089 chr12:46765229-46765244
40	POLR2A	chr12:46761038-46764152	ProgFib	skin:	n/a	n/a
41	MBD4	chr12:46750663-46767066	HepG2	liver:	n/a	n/a
42	POLR2A	chr12:46761151-46764466	GM12891	blood:	n/a	n/a
43	POLR2A	chr12:46761894-46762203	H1-hESC	embryonic stem cell:	n/a	n/a
44	POLR2A	chr12:46760588-46763976	K562	blood:	n/a	n/a
45	POLR2A	chr12:46761501-46762168	HL-60	blood:	n/a	n/a
46	POLR2A	chr12:46760978-46764013	GM12878	blood:	n/a	n/a
47	POLR2A	chr12:46754307-46767479	SK-N-SH	brain:	n/a	n/a
48	POLR2A	chr12:46750204-46767088	U87	brain:	n/a	n/a
49	POLR2A	chr12:46761733-46762117	GM12891	blood:	n/a	n/a
50	POLR2A	chr12:46758610-46767931	HUVEC	blood vessel:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:46652597..46666608-chr12:46757245..46767985,36	MCF-7	breast:
2	chr12:46761697..46764452-chr12:46853963..46855507,2	MCF-7	breast:
3	chr12:46119720..46123062-chr12:46761797..46766025,4	K562	blood:
4	chr12:46761905..46763555-chr15:56533896..56536634,2	MCF-7	breast:
5	chr12:46661733..46663238-chr12:46759583..46762194,2	K562	blood:
6	chr12:46761485..46763714-chr12:46828699..46831336,2	MCF-7	breast:
7	chr12:46672529..46674114-chr12:46761613..46763719,2	MCF-7	breast:

No data

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

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10506267	1.00[EUR][1000 genomes]
rs10506268	1.00[EUR][1000 genomes]
rs11183454	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1125908	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11613912	0.84[AFR][1000 genomes]
rs11830769	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11834593	0.82[ASN][1000 genomes]
rs11834905	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17096884	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2125646	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2307062	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2307063	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2408509	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3742061	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57067899	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57149475	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57271454	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57425661	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60628240	1.00[EUR][1000 genomes]
rs60977966	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61232019	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61406609	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61517444	1.00[EUR][1000 genomes]
rs73282532	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73282561	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73282591	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs74083707	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74083710	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74084031	1.00[EUR][1000 genomes]
rs923788	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]

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	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

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	chr12:46752600-46762400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
4	chr12:46752600-46763000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr12:46752600-46763600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:46752600-46764200	Strong transcription	Fetal Muscle Trunk	muscle
7	chr12:46752800-46762000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr12:46753000-46762600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
9	chr12:46753400-46762400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
10	chr12:46753400-46764200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr12:46753600-46765200	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr12:46754000-46765800	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr12:46754600-46762600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
14	chr12:46754600-46765000	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
15	chr12:46754800-46762600	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr12:46755400-46766000	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr12:46756200-46762200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr12:46756600-46762000	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr12:46756600-46765200	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr12:46756800-46763000	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr12:46756800-46766000	Transcr. at gene 5' and 3'	NHLF	lung
22	chr12:46757000-46763600	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr12:46757400-46762200	Genic enhancers	Placenta Amnion	Placenta Amnion
24	chr12:46757400-46766000	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
25	chr12:46758400-46765200	Transcr. at gene 5' and 3'	HUVEC	blood vessel
26	chr12:46758600-46765000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr12:46758800-46762600	Genic enhancers	Fetal Heart	heart
28	chr12:46758800-46762600	Genic enhancers	K562	blood
29	chr12:46758800-46763800	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
30	chr12:46758800-46763800	Genic enhancers	Fetal Intestine Large	intestine
31	chr12:46758800-46765600	Transcr. at gene 5' and 3'	A549	lung
32	chr12:46758800-46765600	Transcr. at gene 5' and 3'	Osteobl	bone
33	chr12:46758800-46766000	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr12:46758800-46766000	Transcr. at gene 5' and 3'	NHEK	skin
35	chr12:46759000-46762000	Genic enhancers	Fetal Lung	lung
36	chr12:46759000-46764400	Transcr. at gene 5' and 3'	HepG2	liver
37	chr12:46759200-46762400	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
38	chr12:46759600-46764400	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr12:46759600-46765000	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr12:46759600-46765000	Transcr. at gene 5' and 3'	NH-A	brain
41	chr12:46759600-46765200	Transcr. at gene 5' and 3'	Hela-S3	cervix
42	chr12:46759600-46765200	Transcr. at gene 5' and 3'	HMEC	breast
43	chr12:46759800-46762800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr12:46759800-46763000	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr12:46759800-46764400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr12:46760000-46764000	Genic enhancers	Primary monocytes fromperipheralblood	blood
47	chr12:46760200-46765200	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
48	chr12:46760400-46766200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr12:46760600-46762200	Transcr. at gene 5' and 3'	Right Ventricle	heart
50	chr12:46760600-46762600	Genic enhancers	Fetal Thymus	thymus

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