Variant report

Variant	rs7315157
Chromosome Location	chr12:85268543-85268544
allele	A/G
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	ARID3A	chr12:85268354-85268642	K562	blood:	n/a	n/a
2	GTF2F1	chr12:85268458-85268577	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTCF	chr12:85268454-85268610	MCF-7	breast:	n/a	chr12:85268515-85268531 chr12:85268516-85268537 chr12:85268514-85268532 chr12:85268519-85268527
4	CTCF	chr12:85268420-85268570	AG04450	lung:	n/a	chr12:85268515-85268531 chr12:85268516-85268537 chr12:85268514-85268532 chr12:85268519-85268527
5	CEBPB	chr12:85268323-85268623	K562	blood:	n/a	n/a
6	CTCF	chr12:85268195-85268926	IMR90	lung:	n/a	chr12:85268515-85268531 chr12:85268516-85268537 chr12:85268514-85268532 chr12:85268519-85268527
7	CTCF	chr12:85268440-85268590	AoAF	blood vessel:	n/a	chr12:85268515-85268531 chr12:85268516-85268537 chr12:85268514-85268532 chr12:85268519-85268527
8	CTCF	chr12:85268440-85268590	GM12871	blood:	n/a	chr12:85268515-85268531 chr12:85268516-85268537 chr12:85268514-85268532 chr12:85268519-85268527
9	CTCF	chr12:85268480-85268630	NHEK	skin:	n/a	chr12:85268515-85268531 chr12:85268516-85268537 chr12:85268514-85268532 chr12:85268519-85268527
10	ARID3A	chr12:85268279-85268603	HepG2	liver:	n/a	n/a
11	RAD21	chr12:85268239-85268855	HCT-116	colon:	n/a	chr12:85268515-85268534 chr12:85268517-85268524 chr12:85268516-85268530
12	CTCF	chr12:85268500-85268650	GM06990	blood:	n/a	chr12:85268515-85268531 chr12:85268516-85268537 chr12:85268514-85268532 chr12:85268519-85268527
13	CEBPB	chr12:85268168-85268658	A549	lung:	n/a	n/a
14	RAD21	chr12:85268253-85268743	GM12878	blood:	n/a	chr12:85268515-85268534 chr12:85268517-85268524 chr12:85268516-85268530
15	CTCF	chr12:85268460-85268610	BJ	skin:	n/a	chr12:85268515-85268531 chr12:85268516-85268537 chr12:85268514-85268532 chr12:85268519-85268527
16	CTCF	chr12:85268480-85268630	HA-sp	spinal cord:	n/a	chr12:85268515-85268531 chr12:85268516-85268537 chr12:85268514-85268532 chr12:85268519-85268527
17	CTCF	chr12:85268395-85268635	Hela-S3	cervix:	n/a	chr12:85268515-85268531 chr12:85268516-85268537 chr12:85268514-85268532 chr12:85268519-85268527
18	CTCF	chr12:85268460-85268610	HPF	lung:	n/a	chr12:85268515-85268531 chr12:85268516-85268537 chr12:85268514-85268532 chr12:85268519-85268527
19	CTCF	chr12:85268480-85268630	MCF-7	breast:	n/a	chr12:85268515-85268531 chr12:85268516-85268537 chr12:85268514-85268532 chr12:85268519-85268527
20	CTCF	chr12:85267880-85268885	SK-N-SH	brain:	n/a	chr12:85268515-85268531 chr12:85268516-85268537 chr12:85268514-85268532 chr12:85268519-85268527
21	CTCF	chr12:85268460-85268610	NB4	blood:	n/a	chr12:85268515-85268531 chr12:85268516-85268537 chr12:85268514-85268532 chr12:85268519-85268527
22	CTCF	chr12:85268480-85268630	HPF	lung:	n/a	chr12:85268515-85268531 chr12:85268516-85268537 chr12:85268514-85268532 chr12:85268519-85268527
23	CTCF	chr12:85268440-85268590	GM12865	blood:	n/a	chr12:85268515-85268531 chr12:85268516-85268537 chr12:85268514-85268532 chr12:85268519-85268527
24	CTCF	chr12:85268440-85268590	MCF-7	breast:	n/a	chr12:85268515-85268531 chr12:85268516-85268537 chr12:85268514-85268532 chr12:85268519-85268527
25	CTCF	chr12:85268450-85268604	HepG2	liver:	n/a	chr12:85268515-85268531 chr12:85268516-85268537 chr12:85268514-85268532 chr12:85268519-85268527
26	SMC3	chr12:85268346-85269349	Hela-S3	cervix:	n/a	chr12:85268516-85268530
27	MAZ	chr12:85268394-85268565	HepG2	liver:	n/a	n/a
28	CTCF	chr12:85268440-85268590	Hela-S3	cervix:	n/a	chr12:85268515-85268531 chr12:85268516-85268537 chr12:85268514-85268532 chr12:85268519-85268527
29	RAD21	chr12:85268304-85268852	A549	lung:	n/a	chr12:85268515-85268534 chr12:85268517-85268524 chr12:85268516-85268530
30	CEBPB	chr12:85268353-85268653	MCF-7	breast:	n/a	n/a
31	CTCF	chr12:85268395-85268640	LNCaP	prostate:	n/a	chr12:85268515-85268531 chr12:85268516-85268537 chr12:85268514-85268532 chr12:85268519-85268527
32	SMC3	chr12:85268392-85268688	K562	blood:	n/a	chr12:85268516-85268530
33	RAD21	chr12:85268331-85268880	Hela-S3	cervix:	n/a	chr12:85268515-85268534 chr12:85268517-85268524 chr12:85268516-85268530
34	CTCF	chr12:85268440-85268590	GM12872	blood:	n/a	chr12:85268515-85268531 chr12:85268516-85268537 chr12:85268514-85268532 chr12:85268519-85268527
35	ZNF143	chr12:85268331-85268694	GM12878	blood:	n/a	n/a
36	CTCF	chr12:85268420-85268570	HFF	foreskin:	n/a	chr12:85268515-85268531 chr12:85268516-85268537 chr12:85268514-85268532 chr12:85268519-85268527
37	RAD21	chr12:85268419-85268619	HepG2	liver:	n/a	chr12:85268515-85268534 chr12:85268517-85268524 chr12:85268516-85268530
38	MYC	chr12:85268488-85268698	MCF10A-Er-Src	breast:	n/a	n/a
39	CEBPB	chr12:85268175-85268753	A549	lung:	n/a	n/a
40	JUN	chr12:85268291-85268689	K562	blood:	n/a	chr12:85268672-85268684
41	CTCF	chr12:85268440-85268590	GM12874	blood:	n/a	chr12:85268515-85268531 chr12:85268516-85268537 chr12:85268514-85268532 chr12:85268519-85268527
42	CTCF	chr12:85268460-85268610	GM12873	blood:	n/a	chr12:85268515-85268531 chr12:85268516-85268537 chr12:85268514-85268532 chr12:85268519-85268527
43	RAD21	chr12:85268240-85268719	ECC-1	luminal epithelium:	n/a	chr12:85268515-85268534 chr12:85268517-85268524 chr12:85268516-85268530
44	CTCF	chr12:85268440-85268590	NHDF-neo	bronchial:	n/a	chr12:85268515-85268531 chr12:85268516-85268537 chr12:85268514-85268532 chr12:85268519-85268527
45	CTCF	chr12:85268420-85268570	HCT-116	colon:	n/a	chr12:85268515-85268531 chr12:85268516-85268537 chr12:85268514-85268532 chr12:85268519-85268527
46	EBF1	chr12:85268521-85268676	GM12878	blood:	n/a	n/a
47	CTCF	chr12:85268420-85268570	K562	blood:	n/a	chr12:85268515-85268531 chr12:85268516-85268537 chr12:85268514-85268532 chr12:85268519-85268527
48	CEBPB	chr12:85268226-85268674	HCT-116	colon:	n/a	n/a
49	CTCF	chr12:85268460-85268610	AG09309	skin:	n/a	chr12:85268515-85268531 chr12:85268516-85268537 chr12:85268514-85268532 chr12:85268519-85268527
50	CTCF	chr12:85268440-85268590	HVMF	connective:	n/a	chr12:85268515-85268531 chr12:85268516-85268537 chr12:85268514-85268532 chr12:85268519-85268527

Variant related genes	Relation type
SLC6A15	TF binding region

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1016521	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11116642	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11116650	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11116654	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11608668	1.00[ASN][1000 genomes]
rs11836042	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12297157	0.91[YRI][hapmap];0.85[AFR][1000 genomes]
rs12299155	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12316387	0.80[ASW][hapmap];0.95[CEU][hapmap];0.86[GIH][hapmap];0.84[MEX][hapmap];0.83[MKK][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12320882	1.00[ASW][hapmap];0.86[LWK][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes]
rs1525541	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17183612	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2167621	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2404236	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58577207	1.00[ASN][1000 genomes]
rs59913082	1.00[ASN][1000 genomes]
rs6539871	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7295913	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7308326	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73180533	1.00[ASN][1000 genomes]
rs73180540	1.00[ASN][1000 genomes]
rs7960317	0.85[AFR][1000 genomes]
rs7966336	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035863	chr12:84710250-85331290	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv1035236	chr12:84790507-85350433	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv899376	chr12:85157346-85339254	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv899377	chr12:85157346-85629241	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv1040452	chr12:85179586-85747907	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv899378	chr12:85219400-85315865	Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv455666	chr12:85224141-85330496	Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
8	nsv559645	chr12:85224141-85330496	Bivalent/Poised TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
9	nsv470309	chr12:85224141-85339254	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
10	nsv899379	chr12:85226231-85285222	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
11	nsv899380	chr12:85232076-85330496	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
12	nsv899381	chr12:85232076-85339254	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
13	nsv899382	chr12:85232076-85345154	Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
14	nsv559646	chr12:85233731-85330496	Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
15	nsv559647	chr12:85233731-85339254	Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
16	nsv899383	chr12:85233731-85339254	Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
17	nsv899384	chr12:85233731-85345154	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
18	nsv455667	chr12:85249218-85339254	Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
19	nsv559648	chr12:85249218-85339254	Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
20	nsv899385	chr12:85249218-85339254	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
21	nsv899386	chr12:85249218-85345154	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
22	nsv559649	chr12:85257445-85330496	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
23	nsv455668	chr12:85257445-85339254	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
24	nsv559650	chr12:85257445-85339254	Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7315157	PPP1R12A	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:85250000-85271400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr12:85251000-85303000	Weak transcription	NHEK	skin
3	chr12:85251800-85285400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr12:85253800-85271200	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr12:85254000-85276800	Weak transcription	Fetal Brain Male	brain
6	chr12:85254000-85289800	Weak transcription	Brain Angular Gyrus	brain
7	chr12:85254600-85270600	Weak transcription	Brain Substantia Nigra	brain
8	chr12:85254800-85271200	Weak transcription	Brain Hippocampus Middle	brain
9	chr12:85255400-85284200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr12:85257400-85268800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr12:85258400-85268600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr12:85262000-85269200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr12:85267200-85273800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr12:85267200-85274400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr12:85268000-85268600	Enhancers	Hela-S3	cervix
16	chr12:85268200-85274000	Weak transcription	HMEC	breast
17	chr12:85268200-85274800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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