Variant report

Variant	rs4759413
Chromosome Location	chr12:123743436-123743437
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:29)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:29 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:123742924-123744090	GM12878	blood:	n/a	n/a
2	POLR2A	chr12:123742884-123743738	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr12:123742812-123744041	PANC-1	pancreas:	n/a	n/a
4	POLR2A	chr12:123742088-123744024	SK-N-MC	brain:	n/a	n/a
5	POLR2A	chr12:123743261-123744061	PFSK-1	brain:	n/a	n/a
6	POLR2A	chr12:123743273-123743440	GM12878	blood:	n/a	n/a
7	POLR2A	chr12:123742931-123743780	HCT-116	colon:	n/a	n/a
8	POLR2A	chr12:123741683-123743944	HepG2	liver:	n/a	n/a
9	POLR2A	chr12:123742896-123744016	Hela-S3	cervix:	n/a	n/a
10	MAX	chr12:123743250-123743755	K562	blood:	n/a	n/a
11	POLR2A	chr12:123743083-123743820	GM12878	blood:	n/a	n/a
12	CTCF	chr12:123743360-123743510	RPTEC	kidney:	n/a	n/a
13	FOSL2	chr12:123743207-123743797	HepG2	liver:	n/a	n/a
14	POLR2A	chr12:123743263-123743437	MCF10A-Er-Src	breast:	n/a	n/a
15	POLR2A	chr12:123743071-123743460	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr12:123743276-123743941	MCF-7	breast:	n/a	n/a
17	POLR2A	chr12:123743193-123743454	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr12:123742720-123744190	PANC-1	pancreas:	n/a	n/a
19	POLR2A	chr12:123742852-123743992	HepG2	liver:	n/a	n/a
20	POLR2A	chr12:123742947-123743931	SK-N-SH	brain:	n/a	n/a
21	POLR2A	chr12:123742734-123743946	K562	blood:	n/a	n/a
22	POLR2A	chr12:123742464-123744201	PFSK-1	brain:	n/a	n/a
23	POLR2A	chr12:123743139-123743478	HepG2	liver:	n/a	n/a
24	CBX3	chr12:123743351-123743732	K562	blood:	n/a	n/a
25	POLR2A	chr12:123742979-123743757	HepG2	liver:	n/a	n/a
26	POLR2A	chr12:123743216-123743735	HL-60	blood:	n/a	n/a
27	MTA3	chr12:123743101-123743570	GM12878	blood:	n/a	n/a
28	POLR2A	chr12:123743130-123743767	K562	blood:	n/a	n/a
29	POLR2A	chr12:123742051-123744066	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr12:123735647..123738456-chr12:123742871..123745926,3	K562	blood:
2	chr12:123716155..123719079-chr12:123740733..123744668,4	K562	blood:
3	chr12:123737581..123740036-chr12:123741564..123743810,2	MCF-7	breast:
4	chr12:123738852..123742382-chr12:123742428..123743998,3	MCF-7	breast:
5	chr12:123733838..123737944-chr12:123742344..123746385,6	MCF-7	breast:
6	chr12:123740880..123744807-chr12:123747455..123750621,4	MCF-7	breast:
7	chr12:123716188..123719079-chr12:123740733..123744668,4	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CDK2AP1-1	chr12:123743295-123743477	ENSG00000235423.3

No data

Variant related genes	Relation type
ENSG00000269980	TF binding region
ENSG00000051825	Chromatin interaction
ENSG00000130921	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10732573	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs10734901	1.00[ASN][1000 genomes]
rs10744150	0.90[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs10744151	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10744152	1.00[CEU][hapmap];0.89[JPT][hapmap]
rs10772997	0.86[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs10772999	0.89[ASN][1000 genomes]
rs10773002	0.90[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs10846489	0.83[ASN][1000 genomes]
rs10846516	1.00[YRI][hapmap]
rs10846517	0.88[JPT][hapmap]
rs10846519	1.00[CEU][hapmap];0.88[JPT][hapmap]
rs10846520	1.00[CEU][hapmap];0.83[JPT][hapmap]
rs10846523	1.00[CEU][hapmap];0.88[JPT][hapmap]
rs11057202	0.86[ASN][1000 genomes]
rs11057205	0.89[ASN][1000 genomes]
rs11057207	0.89[ASN][1000 genomes]
rs11057209	0.91[ASN][1000 genomes]
rs11057219	0.81[ASN][1000 genomes]
rs11057224	0.82[ASN][1000 genomes]
rs11057239	1.00[YRI][hapmap]
rs11057265	1.00[YRI][hapmap]
rs11057278	1.00[YRI][hapmap]
rs11057287	1.00[CEU][hapmap];0.89[JPT][hapmap]
rs1109559	0.80[ASN][1000 genomes]
rs1109560	0.81[ASN][1000 genomes]
rs11554169	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1568427	0.85[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs1609520	0.91[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs1660	0.84[JPT][hapmap]
rs1727331	0.91[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs1727332	0.80[ASN][1000 genomes]
rs1969355	0.98[ASN][1000 genomes]
rs1980251	1.00[ASN][1000 genomes]
rs2030401	0.82[ASN][1000 genomes]
rs2090764	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2271976	0.82[ASN][1000 genomes]
rs2280424	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28362669	0.89[AFR][1000 genomes]
rs28414347	1.00[CEU][hapmap];0.88[JPT][hapmap]
rs28501453	1.00[CEU][hapmap];0.88[JPT][hapmap]
rs28587386	1.00[CEU][hapmap];0.88[JPT][hapmap]
rs28595660	1.00[CEU][hapmap];0.88[JPT][hapmap]
rs28613486	1.00[CEU][hapmap];0.88[JPT][hapmap]
rs28698461	1.00[YRI][hapmap]
rs36121382	0.94[AFR][1000 genomes]
rs3759111	0.81[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs3759113	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs3759114	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3803001	1.00[CEU][hapmap];0.88[JPT][hapmap]
rs3825141	1.00[CEU][hapmap];0.88[JPT][hapmap]
rs4148864	1.00[YRI][hapmap]
rs4148865	1.00[YRI][hapmap]
rs4460848	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs4474478	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4474479	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4553407	0.82[ASN][1000 genomes]
rs4594040	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4759367	0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs4759372	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4759406	0.94[AFR][1000 genomes]
rs4759407	0.81[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs4759408	1.00[CEU][hapmap];1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs4759411	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4759414	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4759418	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57676984	0.94[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs60077920	0.94[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs60254089	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60296110	0.94[AFR][1000 genomes]
rs61187102	0.88[AFR][1000 genomes]
rs61231969	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61519741	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61953394	0.82[ASN][1000 genomes]
rs6488869	1.00[CEU][hapmap]
rs6488870	1.00[CEU][hapmap]
rs7137286	0.89[ASN][1000 genomes]
rs7297649	1.00[CEU][hapmap];0.88[JPT][hapmap]
rs7304782	0.91[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs7486723	0.85[EUR][1000 genomes]
rs7959415	1.00[CEU][hapmap];0.88[JPT][hapmap]
rs9284166	1.00[CEU][hapmap]
rs9795593	1.00[CEU][hapmap];0.87[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	esv1825473	chr12:123582855-123822503	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv1803368	chr12:123640853-123822503	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
3	esv1830566	chr12:123640853-123822503	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
4	esv1836043	chr12:123709409-123822503	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 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	chr12:123725800-123746400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:123733400-123745000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:123734600-123753200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr12:123735200-123751800	Strong transcription	Fetal Stomach	stomach
5	chr12:123735400-123745400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr12:123735600-123752400	Strong transcription	Thymus	Thymus
7	chr12:123736000-123745400	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr12:123736000-123747800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr12:123736000-123748000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr12:123736000-123752200	Strong transcription	Dnd41	blood
11	chr12:123736200-123744200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr12:123736200-123751400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr12:123736400-123750600	Strong transcription	Fetal Lung	lung
14	chr12:123736400-123752200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr12:123736400-123752600	Strong transcription	NHLF	lung
16	chr12:123737000-123744000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr12:123737000-123753000	Strong transcription	Fetal Intestine Small	intestine
18	chr12:123737200-123752000	Strong transcription	A549	lung
19	chr12:123737400-123749000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr12:123737800-123743800	Strong transcription	GM12878-XiMat	blood
21	chr12:123737800-123745000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr12:123737800-123745600	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr12:123737800-123746800	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr12:123738000-123743600	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr12:123738000-123743600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr12:123738000-123743800	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr12:123738000-123743800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr12:123738000-123744000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr12:123738000-123744600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr12:123738000-123745200	Strong transcription	Spleen	Spleen
31	chr12:123738000-123746000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
32	chr12:123738000-123746200	Strong transcription	H9 Cell Line	embryonic stem cell
33	chr12:123738000-123746200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr12:123738000-123746600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr12:123738000-123748200	Strong transcription	Primary T cells from cord blood	blood
36	chr12:123738000-123749200	Strong transcription	H1 Cell Line	embryonic stem cell
37	chr12:123738000-123749200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr12:123738000-123749600	Strong transcription	Fetal Muscle Leg	muscle
39	chr12:123738000-123749600	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr12:123738000-123750400	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr12:123738000-123751000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr12:123738000-123751200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr12:123738000-123751800	Strong transcription	Liver	Liver
44	chr12:123738000-123751800	Strong transcription	Fetal Intestine Large	intestine
45	chr12:123738000-123752000	Strong transcription	Duodenum Mucosa	Duodenum
46	chr12:123738000-123752000	Strong transcription	HUVEC	blood vessel
47	chr12:123738000-123752600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr12:123738000-123752800	Strong transcription	Placenta Amnion	Placenta Amnion
49	chr12:123738200-123743600	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr12:123738200-123744000	Strong transcription	Lung	lung

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