Variant report

Variant	rs12595717
Chromosome Location	chr15:76477038-76477039
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	GATA3	chr15:76476322-76477551	SK-N-SH	brain:	n/a	chr15:76476655-76476664 chr15:76477129-76477138
2	GATA2	chr15:76475870-76477445	SH-SY5Y	brain:	n/a	chr15:76476655-76476664 chr15:76477129-76477138
3	NFIC	chr15:76476365-76477384	SK-N-SH	brain:	n/a	chr15:76476746-76476762
4	PBX3	chr15:76476375-76477461	SK-N-SH	brain:	n/a	n/a
5	EP300	chr15:76476452-76477322	SK-N-SH_RA	brain:	n/a	n/a
6	JUND	chr15:76476352-76477421	SK-N-SH	brain:	n/a	chr15:76477103-76477117 chr15:76477126-76477138 chr15:76477128-76477136
7	TCF12	chr15:76476338-76477466	SK-N-SH	brain:	n/a	chr15:76477061-76477071
8	EP300	chr15:76476363-76477469	SK-N-SH	brain:	n/a	n/a
9	EP300	chr15:76476385-76477319	SK-N-SH_RA	brain:	n/a	n/a
10	GATA3	chr15:76476210-76477530	SK-N-SH	brain:	n/a	chr15:76476655-76476664 chr15:76477129-76477138
11	GATA3	chr15:76476468-76477389	SH-SY5Y	brain:	n/a	chr15:76476655-76476664 chr15:76477129-76477138
12	TCF12	chr15:76476339-76477530	SK-N-SH	brain:	n/a	chr15:76477061-76477071
13	PBX3	chr15:76476427-76477395	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:76467419..76469629-chr15:76476906..76478729,2	MCF-7	breast:
2	chr15:76476723..76478991-chr15:76480313..76482582,2	K562	blood:

Variant related genes	Relation type
ENSG00000259422	TF binding region

Extended variants
information (count: 108 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs11072576	0.89[CHB][hapmap]
rs11072579	0.81[CHB][hapmap]
rs11072580	0.93[CEU][hapmap];0.95[CHB][hapmap];0.90[EUR][1000 genomes]
rs11072583	0.81[CHB][hapmap]
rs11072585	0.81[CHB][hapmap]
rs11072587	0.81[CHB][hapmap]
rs11633749	0.87[ASN][1000 genomes]
rs11634060	0.81[CHB][hapmap]
rs11636851	0.81[CHB][hapmap]
rs12050896	0.81[CHB][hapmap]
rs12438741	0.90[EUR][1000 genomes]
rs12439484	0.89[CEU][hapmap];0.95[CHB][hapmap];0.82[EUR][1000 genomes]
rs12442266	0.93[CEU][hapmap];0.95[CHB][hapmap];0.83[EUR][1000 genomes]
rs12592501	0.92[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12595211	0.92[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12595738	1.00[CEU][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12898415	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12901160	0.90[CHB][hapmap];0.84[JPT][hapmap];0.90[ASN][1000 genomes]
rs12902506	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12907668	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs12907911	0.83[ASN][1000 genomes]
rs12908334	1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[EUR][1000 genomes]
rs12909718	0.93[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12910640	0.83[JPT][hapmap];0.88[ASN][1000 genomes]
rs12913096	0.92[CEU][hapmap];0.95[CHB][hapmap];0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12916022	0.94[AFR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1474117	0.93[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.82[AFR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16967958	1.00[YRI][hapmap]
rs16968083	0.81[CHB][hapmap]
rs17361504	0.89[CEU][hapmap];0.95[CHB][hapmap];0.82[EUR][1000 genomes]
rs17362383	1.00[YRI][hapmap]
rs17458234	1.00[YRI][hapmap]
rs17460201	1.00[YRI][hapmap]
rs1850722	0.80[CHB][hapmap]
rs1875885	1.00[YRI][hapmap]
rs1875888	0.85[CHB][hapmap]
rs2139190	0.92[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2176623	0.92[CEU][hapmap];0.95[CHB][hapmap];0.83[EUR][1000 genomes]
rs2456045	0.92[CEU][hapmap];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2456046	0.92[CEU][hapmap];0.95[CHB][hapmap]
rs2456050	0.80[CHB][hapmap]
rs2460154	1.00[CEU][hapmap];0.84[JPT][hapmap];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2469541	0.95[CHB][hapmap];0.84[JPT][hapmap]
rs2469542	0.96[CEU][hapmap];0.95[CHB][hapmap];0.83[EUR][1000 genomes]
rs2469548	0.80[CHB][hapmap]
rs2469565	0.91[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2469566	0.92[CEU][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2959850	0.92[CEU][hapmap];0.90[CHB][hapmap];0.90[EUR][1000 genomes]
rs2959853	0.92[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34213321	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34893715	0.94[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs35707798	0.94[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs3759853	0.93[CEU][hapmap];0.95[CHB][hapmap];0.82[EUR][1000 genomes]
rs3866543	1.00[YRI][hapmap]
rs3898352	0.81[CHB][hapmap]
rs4381566	0.82[EUR][1000 genomes]
rs4886484	0.95[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs4886485	0.90[CHB][hapmap];0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs4886488	0.83[CHB][hapmap]
rs4886777	0.80[CHB][hapmap]
rs4886783	0.80[CHB][hapmap]
rs4886787	0.81[CHB][hapmap]
rs4886788	0.81[CHB][hapmap]
rs4886789	0.80[CHB][hapmap]
rs4886791	0.80[CHB][hapmap]
rs67306087	0.91[AFR][1000 genomes]
rs7163036	0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs7174889	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7177923	0.81[CHB][hapmap]
rs7180462	0.80[CHB][hapmap]
rs8028504	0.80[CHB][hapmap]
rs8029637	0.80[CHB][hapmap]
rs8030454	0.81[CHB][hapmap]
rs8033494	0.80[CHB][hapmap]
rs869452	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs870295	0.80[CHB][hapmap]
rs879625	0.81[CHB][hapmap]
rs883993	0.80[CHB][hapmap]
rs937732	0.85[CHB][hapmap]
rs937733	0.81[CHB][hapmap]
rs959991	0.92[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:27 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv569998	chr15:76232605-76550938	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv1048760	chr15:76334544-76496977	Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv833057	chr15:76367848-76585868	ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv1039595	chr15:76431374-76483342	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
5	nsv1045860	chr15:76431374-76485536	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
6	nsv1053643	chr15:76431374-76485966	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
7	nsv1052496	chr15:76432823-76484981	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
8	nsv1036319	chr15:76432823-76489955	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
9	nsv1035806	chr15:76435640-76483342	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
10	nsv1047539	chr15:76435640-76485966	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
11	nsv1042750	chr15:76435640-76490547	ZNF genes & repeats Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
12	nsv1054289	chr15:76437970-76485966	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
13	nsv1035389	chr15:76444695-76483342	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
14	nsv1041435	chr15:76444695-76484981	Bivalent Enhancer ZNF genes & repeats Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
15	nsv1046448	chr15:76444695-76485966	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
16	nsv1046099	chr15:76444695-76490547	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
17	nsv1054300	chr15:76445689-76483342	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
18	nsv1044603	chr15:76445689-76484981	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
19	nsv1043026	chr15:76445689-76485966	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
20	nsv1040683	chr15:76454194-76483342	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
21	nsv1041619	chr15:76454194-76484981	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
22	nsv1046485	chr15:76454194-76485536	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
23	nsv1053572	chr15:76454194-76485966	Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
24	nsv1049916	chr15:76454194-76490547	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
25	nsv1046563	chr15:76460462-76483342	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
26	nsv1053775	chr15:76460462-76485966	Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
27	nsv1054713	chr15:76460462-76505906	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12595717	SCAPER	cis	lung	GTEx

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76443200-76483000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr15:76468000-76478000	Weak transcription	Pancreas	Pancrea
3	chr15:76470600-76482800	Weak transcription	A549	lung
4	chr15:76471000-76478000	Weak transcription	HMEC	breast
5	chr15:76471000-76478200	Weak transcription	Esophagus	oesophagus
6	chr15:76471000-76478200	Weak transcription	Hela-S3	cervix
7	chr15:76471400-76482400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr15:76471600-76478200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr15:76472400-76478200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr15:76473800-76477200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr15:76473800-76478200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr15:76474000-76478200	Weak transcription	HSMM	muscle
13	chr15:76474200-76479800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr15:76475200-76477600	Weak transcription	NHDF-Ad	bronchial
15	chr15:76475200-76477800	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr15:76475200-76477800	Weak transcription	NHLF	lung
17	chr15:76475200-76478200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr15:76475400-76478000	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr15:76475400-76478000	Weak transcription	NH-A	brain
20	chr15:76475400-76478000	Weak transcription	Osteobl	bone
21	chr15:76475400-76478200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr15:76475400-76478400	Weak transcription	HSMMtube	muscle
23	chr15:76475600-76478000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr15:76475800-76477200	Enhancers	Psoas Muscle	Psoas
25	chr15:76476000-76477200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr15:76476000-76477200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr15:76476000-76477200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr15:76476000-76477400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr15:76476200-76477200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr15:76476200-76482600	Weak transcription	Spleen	Spleen
31	chr15:76476400-76477200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr15:76476400-76477200	Enhancers	Fetal Muscle Trunk	muscle
33	chr15:76476400-76482800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr15:76476600-76477200	Enhancers	Fetal Brain Female	brain
35	chr15:76476800-76477200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr15:76476800-76477400	Enhancers	Fetal Brain Male	brain
37	chr15:76477000-76477600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr15:76477000-76478200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr15:76477000-76479600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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