Variant report

Variant	rs653765
Chromosome Location	chr15:59042012-59042013
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	MAX	chr15:59041685-59042656	GM12878	blood:	n/a	chr15:59042042-59042051 chr15:59042041-59042052 chr15:59042042-59042051 chr15:59042042-59042051
2	FOS	chr15:59041993-59042193	MCF10A-Er-Src	breast:	n/a	n/a
3	USF1	chr15:59041687-59042563	A549	lung:	n/a	chr15:59042041-59042052 chr15:59042462-59042478
4	GABPA	chr15:59041716-59042460	MCF-7	breast:	n/a	chr15:59042129-59042140 chr15:59042136-59042145 chr15:59042126-59042140 chr15:59042129-59042138 chr15:59042129-59042143 chr15:59042131-59042140
5	TCF12	chr15:59041603-59042618	ECC-1	luminal epithelium:	n/a	chr15:59042464-59042474
6	SIN3AK20	chr15:59041697-59042096	HepG2	liver:	n/a	n/a
7	CREB1	chr15:59041564-59042616	HepG2	liver:	n/a	n/a
8	POLR2A	chr15:59041579-59042534	K562	blood:	n/a	n/a
9	MXI1	chr15:59040155-59043064	IMR90	lung:	n/a	chr15:59042043-59042052
10	TBL1XR1	chr15:59041339-59042532	K562	blood:	n/a	n/a
11	JUND	chr15:59041805-59042415	H1-hESC	embryonic stem cell:	n/a	chr15:59042213-59042222
12	TBL1XR1	chr15:59041464-59042534	K562	blood:	n/a	n/a
13	MAX	chr15:59040793-59042329	ECC-1	luminal epithelium:	n/a	chr15:59042042-59042051 chr15:59042041-59042052 chr15:59042042-59042051 chr15:59042042-59042051
14	USF1	chr15:59041720-59042380	ECC-1	luminal epithelium:	n/a	chr15:59042041-59042052
15	CREB1	chr15:59041899-59042581	A549	lung:	n/a	n/a
16	BRCA1	chr15:59041763-59042402	Hela-S3	cervix:	n/a	n/a
17	ZNF143	chr15:59041890-59042438	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr15:59041468-59042152	GM12891	blood:	n/a	n/a
19	POLR2A	chr15:59041628-59042557	SK-N-SH	brain:	n/a	n/a
20	BHLHE40	chr15:59041799-59042374	HepG2	liver:	n/a	n/a
21	ATF3	chr15:59041919-59042231	HepG2	liver:	n/a	chr15:59042042-59042062 chr15:59042124-59042133
22	POLR2A	chr15:59041550-59042537	K562	blood:	n/a	n/a
23	POLR2A	chr15:59040941-59042437	A549	lung:	n/a	n/a
24	MAX	chr15:59041864-59042269	K562	blood:	n/a	chr15:59042042-59042051 chr15:59042041-59042052 chr15:59042042-59042051 chr15:59042042-59042051
25	FOS	chr15:59041904-59042259	MCF10A-Er-Src	breast:	n/a	chr15:59042213-59042222
26	JUND	chr15:59040796-59042538	K562	blood:	n/a	chr15:59041444-59041453 chr15:59042213-59042222 chr15:59041417-59041426
27	POLR2A	chr15:59041704-59042586	GM12878	blood:	n/a	n/a
28	MAZ	chr15:59040536-59042601	GM12878	blood:	n/a	chr15:59042042-59042051 chr15:59042041-59042052 chr15:59042042-59042051 chr15:59042042-59042051
29	PML	chr15:59041633-59042570	K562	blood:	n/a	n/a
30	ELF1	chr15:59041685-59042475	MCF-7	breast:	n/a	n/a
31	EP300	chr15:59041847-59042492	GM12878	blood:	n/a	chr15:59042185-59042201 chr15:59042384-59042398 chr15:59042381-59042395
32	TCF7L2	chr15:59041845-59042414	Hela-S3	cervix:	n/a	n/a
33	MYBL2	chr15:59041733-59042082	HepG2	liver:	n/a	n/a
34	TAF1	chr15:59041005-59042389	HepG2	liver:	n/a	n/a
35	BHLHE40	chr15:59040938-59042760	K562	blood:	n/a	chr15:59041307-59041323 chr15:59042462-59042478
36	TCF7L2	chr15:59041629-59042341	HCT-116	colon:	n/a	n/a
37	TAF1	chr15:59041614-59042565	A549	lung:	n/a	n/a
38	E2F6	chr15:59041189-59042366	K562	blood:	n/a	chr15:59042167-59042177 chr15:59042242-59042254 chr15:59042214-59042223 chr15:59041445-59041454 chr15:59041930-59041941 chr15:59042130-59042139 chr15:59041445-59041457 chr15:59041416-59041425
39	GABPA	chr15:59041664-59042496	A549	lung:	n/a	chr15:59042129-59042140 chr15:59042136-59042145 chr15:59042126-59042140 chr15:59042129-59042138 chr15:59042129-59042143 chr15:59042131-59042140
40	ELK1	chr15:59041808-59042371	GM12878	blood:	n/a	n/a
41	POLR2A	chr15:59040911-59042423	GM12878	blood:	n/a	n/a
42	STAT3	chr15:59041981-59042170	MCF10A-Er-Src	breast:	n/a	n/a
43	TAF1	chr15:59041659-59042489	PFSK-1	brain:	n/a	n/a
44	POLR2A	chr15:59041781-59042084	GM12891	blood:	n/a	n/a
45	TAL1	chr15:59041873-59042515	K562	blood:	n/a	n/a
46	YY1	chr15:59041693-59042543	SK-N-SH_RA	brain:	n/a	n/a
47	SIN3AK20	chr15:59041720-59042109	A549	lung:	n/a	n/a
48	YY1	chr15:59041799-59042617	SK-N-SH	brain:	n/a	n/a
49	ZNF143	chr15:59041822-59042447	GM12878	blood:	n/a	n/a
50	MAX	chr15:59041140-59042508	HepG2	liver:	n/a	chr15:59042042-59042051 chr15:59042041-59042052 chr15:59042042-59042051 chr15:59042042-59042051

No.	Distal block	Cell Line	Cell type
1	chr15:59040077..59045685-chr15:59061303..59067063,14	K562	blood:
2	chr15:59041650..59042242-chr3:50336459..50337109,2	Hela-S3	cervix:
3	chr15:59040771..59044388-chr15:59046627..59050183,4	K562	blood:
4	chr15:59040867..59044243-chr15:59224539..59228117,4	K562	blood:
5	chr15:59041505..59042344-chr2:122407188..122408043,2	Hela-S3	cervix:
6	chr1:151881708..151882900-chr15:59041095..59042389,4	Hela-S3	cervix:
7	chr15:59041471..59042418-chr7:5569782..5570300,2	Hela-S3	cervix:
8	chr15:59038832..59043387-chr15:59060936..59065101,7	K562	blood:
9	chr15:59041392..59042094-chr16:56716160..56716780,2	Hela-S3	cervix:
10	chr15:59040618..59043171-chr15:59061931..59064461,2	MCF-7	breast:
11	chr15:59040332..59042868-chr15:59224764..59227201,2	MCF-7	breast:

Variant related genes	Relation type
ADAM10	TF binding region
ENSG00000243477	Chromatin interaction
ENSG00000259173	Chromatin interaction
ENSG00000186792	Chromatin interaction
ENSG00000137776	Chromatin interaction
ENSG00000236859	Chromatin interaction
ENSG00000159445	Chromatin interaction
ENSG00000075624	Chromatin interaction
ENSG00000187193	Chromatin interaction
ENSG00000245975	Chromatin interaction
ENSG00000128923	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10152558	0.83[CHB][hapmap]
rs11854073	0.84[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap]
rs12439457	0.84[ASN][1000 genomes]
rs12911832	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12911961	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12912003	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1427281	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs1427282	0.81[GIH][hapmap]
rs1469343	1.00[YRI][hapmap]
rs1648532	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs17190727	0.81[ASN][1000 genomes]
rs17269397	0.83[CHB][hapmap]
rs2250583	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2555356	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs28864995	0.84[ASW][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap]
rs347115	0.84[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap];0.81[MKK][hapmap];0.82[ASN][1000 genomes]
rs347117	0.92[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.88[ASN][1000 genomes]
rs383902	0.92[ASW][hapmap];0.81[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.81[MKK][hapmap];0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs387812	0.81[MKK][hapmap]
rs442495	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs474875	0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];0.81[MKK][hapmap]
rs4774310	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4775086	0.85[ASW][hapmap];0.83[GIH][hapmap];0.87[LWK][hapmap];0.97[MKK][hapmap];0.95[YRI][hapmap]
rs4775087	0.92[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap]
rs4775094	0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap]
rs507801	0.83[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs514049	0.83[GIH][hapmap]
rs572107	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs585192	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs593742	0.87[CEU][hapmap];0.93[GIH][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs596379	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs602602	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs605928	1.00[ASW][hapmap];0.92[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs610877	0.83[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];0.81[MKK][hapmap]
rs640704	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6494035	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6494036	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6494037	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs673813	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs714696	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7161889	0.92[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.84[ASN][1000 genomes]
rs7163162	0.84[ASN][1000 genomes]
rs7166356	1.00[YRI][hapmap]
rs7171818	0.81[CHB][hapmap]
rs7177678	0.83[GIH][hapmap]
rs7183336	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs8043406	0.81[GIH][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap]
rs972801	0.84[ASW][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051058	chr15:58519922-59092530	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv542401	chr15:58519922-59092530	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	esv34110	chr15:58949991-59381634	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
4	esv1843037	chr15:59005922-59115159	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
5	esv1826703	chr15:59005922-59213678	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
6	esv1798487	chr15:59027139-59213678	Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
7	nsv428638	chr15:59032300-59126567	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs653765	ADAM10	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59037800-59042400	Active TSS	GM12878-XiMat	blood
2	chr15:59037800-59042600	Active TSS	HSMMtube	muscle
3	chr15:59037800-59043000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr15:59038000-59042800	Active TSS	Right Atrium	heart
5	chr15:59038000-59043000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr15:59038200-59042600	Active TSS	NHLF	lung
7	chr15:59038400-59042800	Active TSS	HSMM	muscle
8	chr15:59038400-59043200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr15:59038600-59042800	Active TSS	Right Ventricle	heart
10	chr15:59038800-59042600	Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr15:59038800-59042600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr15:59038800-59043200	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr15:59039000-59042400	Active TSS	Fetal Thymus	thymus
14	chr15:59039000-59042400	Active TSS	Thymus	Thymus
15	chr15:59039000-59042800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr15:59039000-59042800	Active TSS	K562	blood
17	chr15:59039000-59043000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr15:59039000-59043200	Active TSS	NHDF-Ad	bronchial
19	chr15:59039200-59042800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr15:59039400-59042400	Active TSS	HMEC	breast
21	chr15:59039400-59042600	Active TSS	iPS-20b Cell Line	embryonic stem cell
22	chr15:59039400-59042800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr15:59039400-59042800	Active TSS	Aorta	Aorta
24	chr15:59039400-59042800	Active TSS	Fetal Kidney	kidney
25	chr15:59039400-59043000	Active TSS	Rectal Mucosa Donor 29	rectum
26	chr15:59039600-59042400	Active TSS	Fetal Stomach	stomach
27	chr15:59039600-59042600	Active TSS	Brain Substantia Nigra	brain
28	chr15:59039600-59043200	Active TSS	Brain Germinal Matrix	brain
29	chr15:59039800-59042400	Active TSS	NHEK	skin
30	chr15:59039800-59042600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr15:59039800-59042600	Active TSS	Brain Angular Gyrus	brain
32	chr15:59039800-59042600	Active TSS	Duodenum Smooth Muscle	Duodenum
33	chr15:59039800-59042600	Active TSS	Fetal Brain Female	brain
34	chr15:59039800-59042800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr15:59039800-59042800	Active TSS	Brain Hippocampus Middle	brain
36	chr15:59039800-59042800	Active TSS	Brain Inferior Temporal Lobe	brain
37	chr15:59039800-59043000	Active TSS	Brain Cingulate Gyrus	brain
38	chr15:59039800-59043000	Active TSS	Fetal Intestine Large	intestine
39	chr15:59039800-59043200	Active TSS	Stomach Smooth Muscle	stomach
40	chr15:59040000-59042400	Active TSS	H1 Cell Line	embryonic stem cell
41	chr15:59040000-59042400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
42	chr15:59040000-59042400	Active TSS	Fetal Muscle Leg	muscle
43	chr15:59040000-59042400	Active TSS	Skeletal Muscle Female	skeletal muscle
44	chr15:59040000-59042400	Active TSS	Hela-S3	cervix
45	chr15:59040000-59042600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
46	chr15:59040000-59042600	Active TSS	Breast Myoepithelial Primary Cells	Breast
47	chr15:59040000-59042600	Active TSS	NH-A	brain
48	chr15:59040000-59042800	Active TSS	Colonic Mucosa	Colon
49	chr15:59040000-59042800	Active TSS	Fetal Lung	lung
50	chr15:59040000-59043200	Active TSS	ES-I3 Cell Line	embryonic stem cell

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