Variant report

Variant	rs7294563
Chromosome Location	chr12:66429869-66429870
allele	C/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	TCF12	chr12:66428971-66430761	SK-N-SH	brain:	n/a	n/a
2	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
3	ZBTB33	chr12:66429793-66430457	HCT-116	colon:	n/a	n/a
4	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
5	TEAD4	chr12:66429836-66430564	SK-N-SH	brain:	n/a	n/a
6	CTCF	chr12:66429760-66429910	HMF	breast:	n/a	n/a
7	NFIC	chr12:66428962-66430662	SK-N-SH	brain:	n/a	chr12:66429370-66429387 chr12:66429370-66429386
8	TCF12	chr12:66429860-66430764	SK-N-SH	brain:	n/a	n/a
9	EP300	chr12:66429802-66430720	SK-N-SH	brain:	n/a	chr12:66430240-66430254
10	EP300	chr12:66428988-66430752	SK-N-SH	brain:	n/a	chr12:66429463-66429477 chr12:66430240-66430254 chr12:66429720-66429734
11	GATA3	chr12:66429844-66430695	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: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10784513	0.86[AMR][1000 genomes]
rs10784514	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10878367	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10878369	0.90[ASN][1000 genomes]
rs10878370	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11176010	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11176015	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11176016	0.93[ASN][1000 genomes]
rs11176017	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11176018	0.87[ASN][1000 genomes]
rs11176019	0.83[ASN][1000 genomes]
rs11836463	0.91[CEU][hapmap];0.90[CHB][hapmap];0.81[GIH][hapmap]
rs12230818	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12231215	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4130827	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]
rs6581661	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6581662	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7397918	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7961915	0.87[GIH][hapmap];0.93[JPT][hapmap]
rs7975189	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7294563	LLPH	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66425400-66430000	Weak transcription	Psoas Muscle	Psoas
2	chr12:66428800-66431000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr12:66429000-66430800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr12:66429000-66430800	Enhancers	Osteobl	bone
5	chr12:66429000-66431000	Enhancers	Muscle Satellite Cultured Cells	--
6	chr12:66429000-66431000	Enhancers	NHLF	lung
7	chr12:66429200-66430800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr12:66429200-66430800	Enhancers	HUVEC	blood vessel
9	chr12:66429200-66431000	Enhancers	HMEC	breast
10	chr12:66429200-66431000	Enhancers	HSMM	muscle
11	chr12:66429200-66431000	Enhancers	NHDF-Ad	bronchial
12	chr12:66429200-66431800	Enhancers	NHEK	skin
13	chr12:66429400-66430000	Flanking Active TSS	NH-A	brain
14	chr12:66429400-66430200	Enhancers	Placenta Amnion	Placenta Amnion
15	chr12:66429400-66430600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr12:66429400-66430600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr12:66429400-66430600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr12:66429400-66430800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr12:66429400-66431000	Enhancers	Fetal Heart	heart
20	chr12:66429400-66431200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr12:66429400-66432000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr12:66429600-66430600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr12:66429600-66430800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr12:66429600-66430800	Enhancers	Stomach Smooth Muscle	stomach
25	chr12:66429600-66430800	Enhancers	HSMMtube	muscle
26	chr12:66429800-66430600	Enhancers	Fetal Stomach	stomach
27	chr12:66429800-66430600	Enhancers	A549	lung
28	chr12:66429800-66431000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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