Variant report

Variant	rs56308712
Chromosome Location	chr3:136582037-136582038
allele	G/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	USF2	chr3:136581633-136582311	Hela-S3	cervix:	n/a	n/a
2	WRNIP1	chr3:136581526-136582281	GM12878	blood:	n/a	n/a
3	HCFC1	chr3:136580489-136582740	Hela-S3	cervix:	n/a	n/a
4	SIN3A	chr3:136580401-136582142	GM12878	blood:	n/a	chr3:136581090-136581101
5	MXI1	chr3:136580478-136582240	Hela-S3	cervix:	n/a	n/a
6	SIN3A	chr3:136580333-136582090	H1-hESC	embryonic stem cell:	n/a	chr3:136581090-136581101
7	SMC3	chr3:136580605-136582499	Hela-S3	cervix:	n/a	n/a
8	GTF2F1	chr3:136580425-136582168	Hela-S3	cervix:	n/a	n/a
9	CEBPB	chr3:136581416-136582161	A549	lung:	n/a	chr3:136581818-136581830
10	NRF1	chr3:136580406-136582418	SK-N-SH	brain:	n/a	chr3:136580878-136580889 chr3:136581345-136581354
11	ZKSCAN1	chr3:136580538-136582236	Hela-S3	cervix:	n/a	n/a
12	RAD21	chr3:136580781-136582250	Hela-S3	cervix:	n/a	chr3:136581314-136581328
13	MAZ	chr3:136580418-136582115	K562	blood:	n/a	chr3:136581430-136581440
14	POLR2A	chr3:136580401-136582497	GM12878	blood:	n/a	n/a
15	TBP	chr3:136580518-136582483	Hela-S3	cervix:	n/a	n/a
16	KAP1	chr3:136581514-136582076	U2OS	brain:	n/a	n/a
17	STAT3	chr3:136581984-136582175	MCF10A-Er-Src	breast:	n/a	n/a
18	BRCA1	chr3:136580537-136582484	Hela-S3	cervix:	n/a	n/a
19	RFX5	chr3:136580546-136582507	Hela-S3	cervix:	n/a	chr3:136581780-136581789
20	POLR2A	chr3:136580376-136582344	MCF10A-Er-Src	breast:	n/a	n/a
21	PML	chr3:136580155-136582057	GM12878	blood:	n/a	n/a
22	CEBPB	chr3:136580698-136582316	Hela-S3	cervix:	n/a	chr3:136582270-136582282 chr3:136581818-136581830
23	POLR2A	chr3:136580369-136582122	HepG2	liver:	n/a	n/a
24	MXI1	chr3:136580316-136582236	GM12878	blood:	n/a	n/a
25	MXI1	chr3:136579188-136582534	SK-N-SH	brain:	n/a	n/a
26	SIN3AK20	chr3:136580142-136582162	MCF-7	breast:	n/a	n/a
27	MYC	chr3:136581544-136582091	MCF10A-Er-Src	breast:	n/a	n/a
28	MYC	chr3:136580363-136582173	K562	blood:	n/a	chr3:136581430-136581440
29	POLR2A	chr3:136579202-136582111	GM12878	blood:	n/a	n/a
30	RELA	chr3:136580326-136582222	GM18505	blood:	n/a	n/a
31	CEBPB	chr3:136581084-136582192	HepG2	liver:	n/a	chr3:136581818-136581830
32	RCOR1	chr3:136580411-136582282	Hela-S3	cervix:	n/a	n/a
33	MXI1	chr3:136579792-136582381	IMR90	lung:	n/a	n/a
34	POLR2A	chr3:136579161-136582488	GM12891	blood:	n/a	n/a
35	POLR2A	chr3:136580436-136582101	PBDE	blood:	n/a	n/a
36	BHLHE40	chr3:136580853-136582133	HepG2	liver:	n/a	chr3:136581480-136581496
37	RCOR1	chr3:136580410-136582085	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:136471389..136473293-chr3:136580852..136582413,2	MCF-7	breast:
2	chr3:136469311..136474326-chr3:136579207..136583133,7	K562	blood:
3	chr3:136466613..136474326-chr3:136579481..136583133,10	K562	blood:
4	chr3:136556513..136558493-chr3:136581161..136583381,2	K562	blood:
5	chr3:136535239..136537634-chr3:136579848..136582645,2	MCF-7	breast:
6	chr3:136537560..136539935-chr3:136579290..136582081,4	K562	blood:
7	chr3:136536665..136539935-chr3:136579370..136582081,3	K562	blood:
8	chr3:136469358..136473351-chr3:136579831..136582888,9	MCF-7	breast:
9	chr3:136581094..136582950-chr3:136617390..136620227,2	MCF-7	breast:
10	chr3:136581625..136583340-chr3:136586499..136589172,2	K562	blood:

Variant related genes	Relation type
ENSG00000239213	TF binding region
ENSG00000214283	Chromatin interaction
ENSG00000168917	Chromatin interaction
ENSG00000118007	Chromatin interaction
ENSG00000261758	Chromatin interaction
ENSG00000273486	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1048145	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10513016	0.81[EUR][1000 genomes]
rs17301365	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17365351	0.81[EUR][1000 genomes]
rs17366890	0.93[ASN][1000 genomes]
rs17466223	0.81[EUR][1000 genomes]
rs35127615	0.83[AFR][1000 genomes]
rs59361983	0.90[EUR][1000 genomes]
rs59616231	0.81[EUR][1000 genomes]
rs59696368	0.81[EUR][1000 genomes]
rs66471262	0.81[EUR][1000 genomes]
rs67236827	0.81[EUR][1000 genomes]
rs67546863	0.90[EUR][1000 genomes]
rs67923745	0.90[EUR][1000 genomes]
rs68018658	0.82[EUR][1000 genomes]
rs72975363	0.81[EUR][1000 genomes]
rs73230052	0.86[EUR][1000 genomes]
rs73230077	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs73230078	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs73230095	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73231917	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73231937	0.95[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs73231943	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73231944	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73231953	0.91[AFR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73231958	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73231966	0.91[AFR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73231974	0.91[EUR][1000 genomes]
rs73231975	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs923001	0.81[EUR][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	nsv877530	chr3:136514310-136604697	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	n/a
2	nsv877531	chr3:136517016-136662954	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv877532	chr3:136526939-136662603	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv877533	chr3:136539689-136662954	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56308712	IL20RB	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136579200-136582600	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr3:136579400-136582200	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr3:136579400-136582200	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr3:136579400-136582200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr3:136579400-136582400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:136579400-136582400	Active TSS	Colonic Mucosa	Colon
7	chr3:136579400-136582400	Active TSS	Rectal Smooth Muscle	rectum
8	chr3:136579400-136582600	Active TSS	H1 Cell Line	embryonic stem cell
9	chr3:136579400-136582600	Active TSS	NHDF-Ad	bronchial
10	chr3:136579400-136582800	Active TSS	NHLF	lung
11	chr3:136579600-136582200	Active TSS	Fetal Brain Female	brain
12	chr3:136579600-136582400	Active TSS	Right Atrium	heart
13	chr3:136579600-136582600	Active TSS	GM12878-XiMat	blood
14	chr3:136579800-136582200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:136579800-136582200	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr3:136579800-136582200	Active TSS	HSMMtube	muscle
17	chr3:136579800-136582400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr3:136579800-136582400	Active TSS	H9 Cell Line	embryonic stem cell
19	chr3:136579800-136582400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
20	chr3:136579800-136582400	Active TSS	Fetal Intestine Large	intestine
21	chr3:136579800-136582600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
22	chr3:136579800-136582800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr3:136580000-136582200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:136580000-136582200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr3:136580000-136582200	Active TSS	HUES48 Cell Line	embryonic stem cell
26	chr3:136580000-136582200	Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr3:136580000-136582200	Active TSS	Brain Anterior Caudate	brain
28	chr3:136580000-136582200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
29	chr3:136580000-136582200	Active TSS	Colon Smooth Muscle	Colon
30	chr3:136580000-136582200	Active TSS	Esophagus	oesophagus
31	chr3:136580000-136582200	Active TSS	Left Ventricle	heart
32	chr3:136580000-136582200	Active TSS	Small Intestine	intestine
33	chr3:136580000-136582400	Active TSS	ES-I3 Cell Line	embryonic stem cell
34	chr3:136580000-136582400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr3:136580000-136582400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr3:136580000-136582400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr3:136580000-136582400	Active TSS	Psoas Muscle	Psoas
38	chr3:136580000-136582400	Active TSS	Right Ventricle	heart
39	chr3:136580000-136582400	Active TSS	HSMM	muscle
40	chr3:136580000-136582600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr3:136580000-136582600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr3:136580000-136582600	Active TSS	Thymus	Thymus
43	chr3:136580000-136582600	Active TSS	A549	lung
44	chr3:136580000-136582800	Active TSS	HepG2	liver
45	chr3:136580200-136582200	Active TSS	Brain Inferior Temporal Lobe	brain
46	chr3:136580200-136582200	Active TSS	Placenta Amnion	Placenta Amnion
47	chr3:136580200-136582200	Active TSS	Sigmoid Colon	Sigmoid Colon
48	chr3:136580200-136582200	Active TSS	NHEK	skin
49	chr3:136580200-136582400	Active TSS	Fetal Intestine Small	intestine
50	chr3:136580200-136582400	Active TSS	Pancreas	Pancrea

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