Variant report

Variant	rs4759384
Chromosome Location	chr12:123357011-123357012
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:61)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:61 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIN3A	chr12:123356490-123357165	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr12:123356356-123357137	SK-N-MC	brain:	n/a	n/a
3	RXRA	chr12:123356708-123357049	H1-hESC	embryonic stem cell:	n/a	n/a
4	TAF1	chr12:123356580-123357011	H1-neurons	neurons:	n/a	n/a
5	POLR2A	chr12:123356227-123357036	HUVEC	blood vessel:	n/a	n/a
6	CEBPB	chr12:123356539-123357086	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr12:123356580-123357095	H1-hESC	embryonic stem cell:	n/a	n/a
8	MAX	chr12:123356465-123357069	H1-hESC	embryonic stem cell:	n/a	n/a
9	MAX	chr12:123356596-123357058	H1-hESC	embryonic stem cell:	n/a	n/a
10	BACH1	chr12:123356432-123357245	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr12:123356607-123357017	H1-hESC	embryonic stem cell:	n/a	n/a
12	SP4	chr12:123356526-123357100	H1-hESC	embryonic stem cell:	n/a	n/a
13	GABPA	chr12:123356589-123357068	H1-hESC	embryonic stem cell:	n/a	n/a
14	TEAD4	chr12:123356501-123357125	H1-hESC	embryonic stem cell:	n/a	n/a
15	JUND	chr12:123356596-123357117	H1-hESC	embryonic stem cell:	n/a	n/a
16	ZNF274	chr12:123356692-123357041	H1-hESC	embryonic stem cell:	n/a	n/a
17	EGR1	chr12:123356591-123357086	H1-hESC	embryonic stem cell:	n/a	n/a
18	EGR1	chr12:123356585-123357062	H1-hESC	embryonic stem cell:	n/a	n/a
19	JUN	chr12:123356626-123357292	H1-hESC	embryonic stem cell:	n/a	n/a
20	YY1	chr12:123356625-123357158	H1-hESC	embryonic stem cell:	n/a	chr12:123356695-123356706
21	REST	chr12:123356128-123357439	H1-neurons	neurons:	n/a	chr12:123356676-123356689
22	NFIC	chr12:123355889-123357161	GM12878	blood:	n/a	n/a
23	POLR2A	chr12:123356473-123357047	SK-N-MC	brain:	n/a	n/a
24	EP300	chr12:123356589-123357099	H1-hESC	embryonic stem cell:	n/a	chr12:123356589-123356603
25	POLR2A	chr12:123356476-123357360	HUVEC	blood vessel:	n/a	n/a
26	POLR2A	chr12:123356363-123357187	H1-neurons	neurons:	n/a	n/a
27	MTA3	chr12:123356017-123357167	GM12878	blood:	n/a	n/a
28	MXI1	chr12:123355490-123357518	IMR90	lung:	n/a	n/a
29	MXI1	chr12:123355379-123358665	SK-N-SH	brain:	n/a	n/a
30	CTCF	chr12:123356980-123357130	SAEC	small airway:	n/a	n/a
31	NANOG	chr12:123356616-123357063	H1-hESC	embryonic stem cell:	n/a	chr12:123356849-123356858
32	CTBP2	chr12:123356427-123357119	H1-hESC	embryonic stem cell:	n/a	n/a
33	GATA3	chr12:123356482-123357064	T-47D	breast:	n/a	n/a
34	SIN3AK20	chr12:123356523-123357013	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr12:123356203-123357081	HL-60	blood:	n/a	n/a
36	REST	chr12:123356460-123357057	H1-neurons	neurons:	n/a	chr12:123356676-123356689
37	POLR2A	chr12:123356298-123357156	H1-neurons	neurons:	n/a	n/a
38	NANOG	chr12:123356602-123357111	H1-hESC	embryonic stem cell:	n/a	chr12:123356849-123356858
39	MTA3	chr12:123356110-123357085	GM12878	blood:	n/a	n/a
40	ATF2	chr12:123356505-123357148	H1-hESC	embryonic stem cell:	n/a	n/a
41	CHD2	chr12:123356623-123357070	H1-hESC	embryonic stem cell:	n/a	n/a
42	CREB1	chr12:123356637-123357046	H1-hESC	embryonic stem cell:	n/a	n/a
43	TCF12	chr12:123356483-123357276	H1-hESC	embryonic stem cell:	n/a	chr12:123357174-123357182 chr12:123356673-123356681
44	GATA3	chr12:123356583-123357091	T-47D	breast:	n/a	n/a
45	SP1	chr12:123356480-123357269	H1-hESC	embryonic stem cell:	n/a	chr12:123356697-123356706
46	MXI1	chr12:123356548-123357167	H1-hESC	embryonic stem cell:	n/a	n/a
47	HDAC2	chr12:123356495-123357041	H1-hESC	embryonic stem cell:	n/a	n/a
48	MYC	chr12:123356000-123357043	NB4	blood:	n/a	n/a
49	POLR2A	chr12:123356274-123357502	PANC-1	pancreas:	n/a	n/a
50	TEAD4	chr12:123356605-123357029	H1-hESC	embryonic stem cell:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr12:123356440..123358585-chr12:123360097..123361963,2	K562	blood:
2	chr12:123355640..123358495-chr12:123449218..123452212,2	MCF-7	breast:
3	chr12:123356727..123361663-chr12:123362714..123365634,4	K562	blood:
4	chr12:123318632..123320877-chr12:123355595..123357643,2	MCF-7	breast:
5	chr12:123356737..123358240-chr12:123467000..123469929,2	MCF-7	breast:
6	chr12:123353502..123357222-chr12:123371821..123375830,5	MCF-7	breast:
7	chr12:123356529..123360323-chr12:123367921..123371522,3	K562	blood:

No data

Variant related genes	Relation type
VPS37B	TF binding region
ENSG00000130787	Chromatin interaction
ENSG00000150967	Chromatin interaction
ENSG00000139722	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1026395	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][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]
rs1037593	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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]
rs10744394	0.88[EUR][1000 genomes]
rs10744439	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10773599	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10847742	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10847749	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10847751	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10847775	1.00[JPT][hapmap]
rs10847910	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10848148	1.00[JPT][hapmap]
rs10848363	1.00[JPT][hapmap]
rs10848365	1.00[JPT][hapmap]
rs11059729	0.86[CEU][hapmap]
rs11060152	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11060211	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11060932	1.00[JPT][hapmap]
rs11060999	1.00[JPT][hapmap]
rs11610441	1.00[MEX][hapmap]
rs12311043	1.00[JPT][hapmap]
rs1260121	1.00[JPT][hapmap]
rs1671684	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1671686	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1671687	1.00[JPT][hapmap]
rs1696327	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1798563	1.00[JPT][hapmap]
rs1975761	1.00[JPT][hapmap]
rs2061099	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2271048	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2343107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2649895	1.00[JPT][hapmap]
rs2649896	1.00[JPT][hapmap]
rs2649903	1.00[JPT][hapmap]
rs2649904	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2656812	1.00[JPT][hapmap]
rs3844369	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4307760	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4759351	0.96[EUR][1000 genomes]
rs4759352	0.96[EUR][1000 genomes]
rs4759353	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4759354	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4759388	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4759438	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[TSI][hapmap]
rs651683	1.00[JPT][hapmap]
rs7138257	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][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]
rs7298176	1.00[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7306047	0.88[CEU][hapmap];0.83[GIH][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7306948	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7485652	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7957643	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7958155	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs839354	1.00[JPT][hapmap]
rs897384	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs897388	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs937765	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs967281	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9795629	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899571	chr12:123215734-123363562	Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3388790	chr12:123275902-123655103	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv899572	chr12:123292503-123477311	Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv899573	chr12:123312051-123528405	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv517200	chr12:123312051-123654498	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
6	nsv899574	chr12:123316566-123360151	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv899575	chr12:123326374-123360151	Weak transcription Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
8	nsv899576	chr12:123335527-123528405	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123353000-123358600	Weak transcription	HepG2	liver
2	chr12:123354800-123359000	Enhancers	Small Intestine	intestine
3	chr12:123355000-123357400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
4	chr12:123355200-123357800	Enhancers	Sigmoid Colon	Sigmoid Colon
5	chr12:123355200-123358000	Weak transcription	Gastric	stomach
6	chr12:123355200-123359000	Enhancers	Lung	lung
7	chr12:123355200-123359200	Enhancers	Spleen	Spleen
8	chr12:123355400-123357200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr12:123355400-123357200	Flanking Active TSS	Primary hematopoietic stem cells	blood
10	chr12:123355400-123357200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr12:123355400-123357200	Flanking Active TSS	Fetal Brain Female	brain
12	chr12:123355400-123357200	Flanking Active TSS	Rectal Smooth Muscle	rectum
13	chr12:123355400-123357200	Flanking Active TSS	Stomach Smooth Muscle	stomach
14	chr12:123355400-123357200	Flanking Active TSS	HUVEC	blood vessel
15	chr12:123355400-123357800	Flanking Active TSS	Adipose Nuclei	Adipose
16	chr12:123355400-123357800	Flanking Active TSS	HSMMtube	muscle
17	chr12:123355400-123359000	Enhancers	Psoas Muscle	Psoas
18	chr12:123355600-123357200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr12:123355600-123357200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr12:123355600-123357200	Flanking Active TSS	Fetal Muscle Leg	muscle
21	chr12:123355600-123357200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
22	chr12:123355600-123357200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
23	chr12:123355600-123357200	Flanking Active TSS	NH-A	brain
24	chr12:123355600-123357400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr12:123355600-123357400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr12:123355600-123357400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
27	chr12:123355600-123357400	Flanking Active TSS	NHDF-Ad	bronchial
28	chr12:123355600-123357600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
29	chr12:123355600-123357600	Flanking Active TSS	Brain Anterior Caudate	brain
30	chr12:123355600-123357600	Flanking Active TSS	Brain Cingulate Gyrus	brain
31	chr12:123355600-123357600	Flanking Active TSS	Right Atrium	heart
32	chr12:123355600-123357800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr12:123355600-123358200	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
34	chr12:123355600-123359400	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
35	chr12:123355800-123357200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
36	chr12:123355800-123357200	Flanking Active TSS	Colon Smooth Muscle	Colon
37	chr12:123355800-123357200	Flanking Active TSS	Duodenum Mucosa	Duodenum
38	chr12:123355800-123357200	Flanking Active TSS	HSMM	muscle
39	chr12:123355800-123357200	Flanking Active TSS	NHLF	lung
40	chr12:123355800-123357400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
41	chr12:123355800-123357600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr12:123355800-123357800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr12:123355800-123357800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr12:123355800-123358000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
45	chr12:123355800-123358400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr12:123355800-123358800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
47	chr12:123355800-123359000	Enhancers	Pancreas	Pancrea
48	chr12:123355800-123363600	Weak transcription	Dnd41	blood
49	chr12:123356000-123357200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
50	chr12:123356000-123357200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain

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