Variant report

Variant	rs4130827
Chromosome Location	chr12:66430452-66430453
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	STAT3	chr12:66430111-66430605	MCF10A-Er-Src	breast:	n/a	chr12:66430396-66430407
2	NFIC	chr12:66429929-66430615	SK-N-SH	brain:	n/a	n/a
3	RXRA	chr12:66429960-66430663	SK-N-SH	brain:	n/a	n/a
4	RAD21	chr12:66430285-66430485	Hela-S3	cervix:	n/a	n/a
5	MAZ	chr12:66429968-66430684	IMR90	lung:	n/a	n/a
6	MAX	chr12:66430034-66430659	SK-N-SH	brain:	n/a	n/a
7	TCF12	chr12:66428971-66430761	SK-N-SH	brain:	n/a	n/a
8	FOSL2	chr12:66430035-66430540	A549	lung:	n/a	n/a
9	JUND	chr12:66429983-66430766	SK-N-SH	brain:	n/a	n/a
10	FOXA2	chr12:66430075-66430456	A549	lung:	n/a	n/a
11	MEF2A	chr12:66429098-66430715	SK-N-SH	brain:	n/a	chr12:66430235-66430246 chr12:66429821-66429842 chr12:66430234-66430248 chr12:66430229-66430250 chr12:66429313-66429321 chr12:66430229-66430250 chr12:66429824-66429835
12	RAD21	chr12:66429926-66430614	ECC-1	luminal epithelium:	n/a	chr12:66430146-66430160
13	ZBTB33	chr12:66429793-66430457	HCT-116	colon:	n/a	n/a
14	STAT3	chr12:66430121-66430585	MCF10A-Er-Src	breast:	n/a	chr12:66430396-66430407
15	TEAD4	chr12:66429947-66430689	ECC-1	luminal epithelium:	n/a	n/a
16	STAT3	chr12:66430238-66430484	MCF10A-Er-Src	breast:	n/a	chr12:66430396-66430407
17	NR3C1	chr12:66430072-66430503	ECC-1	luminal epithelium:	n/a	n/a
18	SP1	chr12:66430093-66430488	A549	lung:	n/a	n/a
19	MEF2A	chr12:66429764-66430657	SK-N-SH	brain:	n/a	chr12:66430235-66430246 chr12:66429821-66429842 chr12:66430234-66430248 chr12:66430229-66430250 chr12:66430229-66430250 chr12:66429824-66429835
20	FOS	chr12:66430116-66430656	MCF10A-Er-Src	breast:	n/a	n/a
21	STAT3	chr12:66430122-66430622	MCF10A-Er-Src	breast:	n/a	chr12:66430396-66430407
22	EP300	chr12:66430012-66430514	SK-N-SH_RA	brain:	n/a	chr12:66430240-66430254
23	TCF12	chr12:66429898-66430636	ECC-1	luminal epithelium:	n/a	n/a
24	TEAD4	chr12:66429836-66430564	SK-N-SH	brain:	n/a	n/a
25	NFIC	chr12:66429955-66430695	ECC-1	luminal epithelium:	n/a	n/a
26	TEAD4	chr12:66429896-66430713	SK-N-SH	brain:	n/a	n/a
27	SRF	chr12:66429966-66430661	ECC-1	luminal epithelium:	n/a	chr12:66430201-66430211
28	RXRA	chr12:66429961-66430583	SK-N-SH	brain:	n/a	n/a
29	PBX3	chr12:66429962-66430710	SK-N-SH	brain:	n/a	n/a
30	NFIC	chr12:66428962-66430662	SK-N-SH	brain:	n/a	chr12:66429370-66429387 chr12:66429370-66429386
31	RAD21	chr12:66430020-66430507	IMR90	lung:	n/a	chr12:66430146-66430160
32	POLR2A	chr12:66430016-66430560	U87	brain:	n/a	n/a
33	POLR2A	chr12:66430189-66430572	SK-N-SH	brain:	n/a	n/a
34	TCF12	chr12:66429860-66430764	SK-N-SH	brain:	n/a	n/a
35	EP300	chr12:66429903-66430864	ECC-1	luminal epithelium:	n/a	chr12:66430240-66430254
36	MYC	chr12:66430150-66430483	MCF10A-Er-Src	breast:	n/a	n/a
37	MYC	chr12:66430150-66430552	MCF10A-Er-Src	breast:	n/a	n/a
38	SP1	chr12:66429919-66430681	HCT-116	colon:	n/a	n/a
39	FOS	chr12:66430146-66430625	MCF10A-Er-Src	breast:	n/a	n/a
40	EP300	chr12:66430077-66430498	SK-N-SH_RA	brain:	n/a	chr12:66430240-66430254
41	POLR2A	chr12:66429995-66430610	SK-N-SH	brain:	n/a	n/a
42	NR3C1	chr12:66430080-66430453	ECC-1	luminal epithelium:	n/a	n/a
43	EP300	chr12:66429802-66430720	SK-N-SH	brain:	n/a	chr12:66430240-66430254
44	EP300	chr12:66428988-66430752	SK-N-SH	brain:	n/a	chr12:66429463-66429477 chr12:66430240-66430254 chr12:66429720-66429734
45	STAT3	chr12:66430127-66430585	MCF10A-Er-Src	breast:	n/a	chr12:66430396-66430407
46	FOSL2	chr12:66430098-66430507	SK-N-SH	brain:	n/a	n/a
47	FOSL2	chr12:66429877-66430664	SK-N-SH	brain:	n/a	n/a
48	TCF12	chr12:66429920-66430672	ECC-1	luminal epithelium:	n/a	n/a
49	SIN3AK20	chr12:66430005-66430505	SK-N-SH	brain:	n/a	n/a
50	GATA3	chr12:66429909-66430717	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000213343	TF binding region

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10784514	0.87[ASN][1000 genomes]
rs10878367	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10878369	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10878370	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11176010	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11176015	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11176016	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11176017	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11176018	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11176019	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11836463	0.91[CEU][hapmap];0.90[CHB][hapmap];0.91[GIH][hapmap];0.82[EUR][1000 genomes]
rs12230818	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12231215	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6581661	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6581662	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7294563	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7397918	0.83[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7961915	0.93[JPT][hapmap]
rs7975189	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052503	chr12:66293898-67269495	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv541515	chr12:66293898-67269495	Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv899213	chr12:66389968-66500036	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
4	nsv832446	chr12:66393863-66501484	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1049537	chr12:66403269-66606174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv975508	chr12:66430304-66435114	Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66428800-66431000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr12:66429000-66430800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr12:66429000-66430800	Enhancers	Osteobl	bone
4	chr12:66429000-66431000	Enhancers	Muscle Satellite Cultured Cells	--
5	chr12:66429000-66431000	Enhancers	NHLF	lung
6	chr12:66429200-66430800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr12:66429200-66430800	Enhancers	HUVEC	blood vessel
8	chr12:66429200-66431000	Enhancers	HMEC	breast
9	chr12:66429200-66431000	Enhancers	HSMM	muscle
10	chr12:66429200-66431000	Enhancers	NHDF-Ad	bronchial
11	chr12:66429200-66431800	Enhancers	NHEK	skin
12	chr12:66429400-66430600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr12:66429400-66430600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr12:66429400-66430600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr12:66429400-66430800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr12:66429400-66431000	Enhancers	Fetal Heart	heart
17	chr12:66429400-66431200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr12:66429400-66432000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr12:66429600-66430600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr12:66429600-66430800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr12:66429600-66430800	Enhancers	Stomach Smooth Muscle	stomach
22	chr12:66429600-66430800	Enhancers	HSMMtube	muscle
23	chr12:66429800-66430600	Enhancers	Fetal Stomach	stomach
24	chr12:66429800-66430600	Enhancers	A549	lung
25	chr12:66429800-66431000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr12:66430000-66430600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr12:66430000-66430600	Enhancers	Colon Smooth Muscle	Colon
28	chr12:66430000-66430600	Enhancers	Fetal Muscle Leg	muscle
29	chr12:66430000-66430600	Enhancers	Left Ventricle	heart
30	chr12:66430000-66430600	Enhancers	Psoas Muscle	Psoas
31	chr12:66430000-66430600	Enhancers	HepG2	liver
32	chr12:66430000-66430800	Enhancers	NH-A	brain
33	chr12:66430200-66430600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr12:66430400-66430600	Enhancers	Skeletal Muscle Male	skeletal muscle

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