Variant report

Variant	rs60371615
Chromosome Location	chr15:76478500-76478501
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	RAD21	chr15:76477821-76478542	HCT-116	colon:	n/a	n/a
2	RAD21	chr15:76477913-76478548	A549	lung:	n/a	n/a
3	RAD21	chr15:76477955-76478541	ECC-1	luminal epithelium:	n/a	n/a
4	CTCF	chr15:76478380-76478530	HEK293	kidney:	n/a	n/a
5	CTCF	chr15:76477987-76478513	K562	blood:	n/a	n/a
6	POLR2A	chr15:76478032-76478985	Hela-S3	cervix:	n/a	n/a
7	CTCF	chr15:76477637-76478596	A549	lung:	n/a	n/a
8	CTCF	chr15:76478360-76478510	GM12871	blood:	n/a	n/a
9	FOSL2	chr15:76478095-76478710	SK-N-SH	brain:	n/a	chr15:76478417-76478427 chr15:76478417-76478427 chr15:76478417-76478427 chr15:76478604-76478612 chr15:76478418-76478426
10	CTCF	chr15:76477851-76478632	HCT-116	colon:	n/a	n/a
11	CTCF	chr15:76478400-76478550	Hela-S3	cervix:	n/a	n/a
12	RAD21	chr15:76477960-76478548	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:76478115..76478633-chr15:76622409..76623267,2	MCF-7	breast:
2	chr15:76478027..76479862-chr15:76483019..76485634,3	MCF-7	breast:
3	chr15:76467419..76469629-chr15:76476906..76478729,2	MCF-7	breast:
4	chr15:76478149..76479732-chr15:76481760..76484387,3	K562	blood:
5	chr15:76476723..76478991-chr15:76480313..76482582,2	K562	blood:
6	chr15:76477747..76478594-chr15:76625784..76626375,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259422	TF binding region
ENSG00000169758	Chromatin interaction

Extended variants
information (count: 119 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs11072576	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11072577	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11072578	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11072579	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11072583	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11072585	0.88[AFR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11072587	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11629459	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11631690	0.85[EUR][1000 genomes]
rs11631764	0.85[EUR][1000 genomes]
rs11631874	0.86[EUR][1000 genomes]
rs11633405	0.84[EUR][1000 genomes]
rs11634060	0.83[EUR][1000 genomes]
rs11634472	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11634796	0.81[EUR][1000 genomes]
rs11636278	0.84[EUR][1000 genomes]
rs11636851	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11637473	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11637855	0.90[AFR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12050813	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12050896	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12443449	0.83[EUR][1000 genomes]
rs12901160	0.81[ASN][1000 genomes]
rs12902506	0.82[ASN][1000 genomes]
rs16968083	0.84[EUR][1000 genomes]
rs1850722	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1875887	0.97[ASN][1000 genomes]
rs1875888	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2007928	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2016734	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2404974	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2456049	0.99[ASN][1000 genomes]
rs2456050	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2456057	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2456071	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2469548	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2469565	0.80[ASN][1000 genomes]
rs2469566	0.80[ASN][1000 genomes]
rs2938697	0.84[ASN][1000 genomes]
rs2959853	0.80[ASN][1000 genomes]
rs35831705	0.92[AFR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3784449	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3898352	0.97[AFR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3915459	0.83[EUR][1000 genomes]
rs3915460	0.83[EUR][1000 genomes]
rs3927264	0.82[EUR][1000 genomes]
rs3958426	0.84[EUR][1000 genomes]
rs3991792	0.83[EUR][1000 genomes]
rs3991793	0.83[EUR][1000 genomes]
rs3991794	0.84[EUR][1000 genomes]
rs4592616	0.88[EUR][1000 genomes]
rs4886486	0.83[EUR][1000 genomes]
rs4886487	0.84[EUR][1000 genomes]
rs4886488	0.83[EUR][1000 genomes]
rs4886777	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4886779	0.87[AFR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4886781	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4886783	0.97[AFR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4886784	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4886787	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4886789	0.86[EUR][1000 genomes]
rs4886791	0.83[EUR][1000 genomes]
rs5012144	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55805818	0.88[AFR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56737606	0.85[EUR][1000 genomes]
rs57182285	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60017340	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60290059	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60561507	0.80[EUR][1000 genomes]
rs61018254	0.83[EUR][1000 genomes]
rs61275737	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61300240	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62027018	0.84[EUR][1000 genomes]
rs62027047	0.82[EUR][1000 genomes]
rs62027048	0.83[EUR][1000 genomes]
rs62030232	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62030246	0.92[AFR][1000 genomes]
rs6495197	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7174889	0.83[ASN][1000 genomes]
rs7177923	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7179750	0.84[EUR][1000 genomes]
rs7180462	0.84[EUR][1000 genomes]
rs8028504	0.84[EUR][1000 genomes]
rs8029637	0.84[EUR][1000 genomes]
rs8030454	0.84[EUR][1000 genomes]
rs8033494	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8039063	0.86[EUR][1000 genomes]
rs870295	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs879625	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs883993	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs937732	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs937733	0.95[EUR][1000 genomes];0.93[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs60371615	ISL2	Cis_1M	lymphoblastoid	RTeQTL
rs60371615	SCAPER	cis	Whole Blood	GTEx
rs60371615	SCAPER	cis	lung	GTEx
rs60371615	SCAPER	Cis_1M	lymphoblastoid	RTeQTL
rs60371615	SCAPER	cis	Thyroid	GTEx
rs60371615	RP11-593F23.1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:45 , 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	chr15:76470600-76482800	Weak transcription	A549	lung
3	chr15:76471400-76482400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr15:76474200-76479800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr15:76476200-76482600	Weak transcription	Spleen	Spleen
6	chr15:76476400-76482800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr15:76477000-76479600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr15:76477200-76480000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr15:76477200-76480000	Weak transcription	Fetal Brain Female	brain
10	chr15:76477400-76479600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:76477600-76478800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr15:76477600-76479000	Enhancers	NHDF-Ad	bronchial
13	chr15:76477800-76478800	Enhancers	Muscle Satellite Cultured Cells	--
14	chr15:76477800-76478800	Enhancers	HepG2	liver
15	chr15:76477800-76479000	Enhancers	NHLF	lung
16	chr15:76477800-76479200	Enhancers	Stomach Mucosa	stomach
17	chr15:76477800-76479800	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr15:76478000-76478600	Enhancers	Pancreas	Pancrea
19	chr15:76478000-76478800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr15:76478000-76478800	Enhancers	HMEC	breast
21	chr15:76478000-76478800	Enhancers	NH-A	brain
22	chr15:76478000-76479000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr15:76478000-76479200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr15:76478000-76479800	Enhancers	Psoas Muscle	Psoas
25	chr15:76478200-76478600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr15:76478200-76478600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr15:76478200-76478600	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr15:76478200-76478600	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr15:76478200-76478600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr15:76478200-76478600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr15:76478200-76478600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr15:76478200-76478600	Enhancers	Placenta	Placenta
33	chr15:76478200-76478600	Enhancers	Placenta Amnion	Placenta Amnion
34	chr15:76478200-76478800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr15:76478200-76478800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr15:76478200-76478800	Enhancers	Hela-S3	cervix
37	chr15:76478200-76478800	Enhancers	HUVEC	blood vessel
38	chr15:76478200-76478800	Enhancers	NHEK	skin
39	chr15:76478200-76479000	Enhancers	HSMM	muscle
40	chr15:76478200-76480000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
41	chr15:76478200-76480200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr15:76478200-76488400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr15:76478400-76478600	Enhancers	Right Atrium	heart
44	chr15:76478400-76478600	Enhancers	HSMMtube	muscle
45	chr15:76478400-76478800	Enhancers	Osteobl	bone

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