Variant report

Variant	rs3861181
Chromosome Location	chr15:79043370-79043371
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	EBF1	chr15:79043315-79043645	GM12878	blood:	n/a	n/a
2	POLR2A	chr15:79043342-79043439	A549	lung:	n/a	n/a
3	RAD21	chr15:79043354-79043732	SK-N-SH_RA	brain:	n/a	n/a
4	CTCF	chr15:79043290-79043827	MCF-7	breast:	n/a	chr15:79043461-79043474
5	HCFC1	chr15:79043059-79043907	Hela-S3	cervix:	n/a	n/a
6	GTF2F1	chr15:79043332-79043670	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr15:79043354-79043452	A549	lung:	n/a	n/a
8	CTCF	chr15:79043220-79043370	GM12864	blood:	n/a	n/a
9	TEAD4	chr15:79043349-79043774	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr15:79043169-79043637	U87	brain:	n/a	n/a
11	TCF3	chr15:79043361-79043673	GM12878	blood:	n/a	chr15:79043646-79043655 chr15:79043643-79043659
12	POLR2A	chr15:79043344-79043473	Gliobla	brain:	n/a	n/a
13	CTCF	chr15:79043296-79043757	MCF-7	breast:	n/a	chr15:79043461-79043474
14	MAX	chr15:79043292-79043711	Hela-S3	cervix:	n/a	chr15:79043538-79043548
15	SP1	chr15:79043286-79043784	GM12878	blood:	n/a	chr15:79043538-79043548 chr15:79043483-79043493 chr15:79043537-79043549 chr15:79043502-79043513 chr15:79043483-79043493 chr15:79043537-79043548 chr15:79043537-79043549
16	POLR2A	chr15:79043294-79043665	Hela-S3	cervix:	n/a	n/a
17	E2F4	chr15:79043113-79043655	MCF10A-Er-Src	breast:	n/a	n/a
18	SP1	chr15:79043199-79043798	A549	lung:	n/a	chr15:79043538-79043548 chr15:79043483-79043493 chr15:79043537-79043549 chr15:79043502-79043513 chr15:79043483-79043493 chr15:79043537-79043548 chr15:79043537-79043549
19	POLR2A	chr15:79043309-79043606	A549	lung:	n/a	n/a
20	TAF1	chr15:79043251-79043540	Hela-S3	cervix:	n/a	n/a
21	POU2F2	chr15:79043333-79043751	GM12878	blood:	n/a	n/a
22	MAZ	chr15:79043243-79043804	IMR90	lung:	n/a	chr15:79043538-79043548
23	RAD21	chr15:79043285-79043800	A549	lung:	n/a	n/a
24	RAD21	chr15:79043319-79043798	HepG2	liver:	n/a	n/a
25	SMC3	chr15:79043190-79043962	SK-N-SH	brain:	n/a	n/a
26	STAT3	chr15:79043028-79043417	MCF10A-Er-Src	breast:	n/a	n/a
27	POLR2A	chr15:79043329-79043434	MCF10A-Er-Src	breast:	n/a	n/a
28	POLR2A	chr15:79043290-79043485	A549	lung:	n/a	n/a
29	POLR2A	chr15:79043279-79043588	HCT-116	colon:	n/a	n/a
30	RAD21	chr15:79043261-79043899	HCT-116	colon:	n/a	n/a
31	SP1	chr15:79043298-79043676	GM12878	blood:	n/a	chr15:79043538-79043548 chr15:79043483-79043493 chr15:79043537-79043549 chr15:79043502-79043513 chr15:79043483-79043493 chr15:79043537-79043548 chr15:79043537-79043549
32	CTCF	chr15:79043286-79043859	A549	lung:	n/a	chr15:79043461-79043474
33	RAD21	chr15:79043277-79043891	HCT-116	colon:	n/a	n/a
34	SP1	chr15:79043323-79043693	H1-hESC	embryonic stem cell:	n/a	chr15:79043538-79043548 chr15:79043483-79043493 chr15:79043537-79043549 chr15:79043502-79043513 chr15:79043483-79043493 chr15:79043537-79043548 chr15:79043537-79043549
35	SMC3	chr15:79043116-79043779	Hela-S3	cervix:	n/a	n/a
36	CTCF	chr15:79043320-79043729	H1-hESC	embryonic stem cell:	n/a	chr15:79043461-79043474
37	RAD21	chr15:79043368-79043715	H1-hESC	embryonic stem cell:	n/a	n/a
38	RAD21	chr15:79043319-79043750	ECC-1	luminal epithelium:	n/a	n/a
39	RAD21	chr15:79043294-79043813	ECC-1	luminal epithelium:	n/a	n/a
40	STAT3	chr15:79043151-79043615	MCF10A-Er-Src	breast:	n/a	n/a
41	POLR2A	chr15:79043223-79043578	Hela-S3	cervix:	n/a	n/a
42	POLR2A	chr15:79043230-79043532	HCT-116	colon:	n/a	n/a
43	RAD21	chr15:79043291-79043807	MCF-7	breast:	n/a	n/a
44	SP1	chr15:79043341-79043661	H1-hESC	embryonic stem cell:	n/a	chr15:79043538-79043548 chr15:79043483-79043493 chr15:79043537-79043549 chr15:79043502-79043513 chr15:79043483-79043493 chr15:79043537-79043548 chr15:79043537-79043549
45	POLR2A	chr15:79043259-79043670	HUVEC	blood vessel:	n/a	n/a
46	RAD21	chr15:79043296-79043786	SK-N-SH_RA	brain:	n/a	n/a
47	FOXP2	chr15:79043337-79043635	PFSK-1	brain:	n/a	n/a
48	POLR2A	chr15:79043282-79043557	ECC-1	luminal epithelium:	n/a	n/a
49	ZNF263	chr15:79043319-79043723	HEK293-T-REx	kidney:	n/a	n/a
50	SP1	chr15:79043326-79043731	K562	blood:	n/a	chr15:79043538-79043548 chr15:79043483-79043493 chr15:79043537-79043549 chr15:79043502-79043513 chr15:79043483-79043493 chr15:79043537-79043548 chr15:79043537-79043549

No.	Distal block	Cell Line	Cell type
1	chr15:78774775..78775285-chr15:79043113..79043866,2	MCF-7	breast:
2	chr15:78591118..78593802-chr15:79042531..79044066,2	K562	blood:
3	chr15:78292186..78292985-chr15:79043320..79043997,6	MCF-7	breast:
4	chr15:78292246..78292984-chr15:79043169..79044003,5	MCF-7	breast:
5	chr15:78292248..78292748-chr15:79043024..79043675,2	Hela-S3	cervix:
6	chr15:78291849..78292957-chr15:79043056..79044329,6	K562	blood:
7	chr15:79006871..79007822-chr15:79043105..79043707,3	K562	blood:
8	chr15:79006813..79007487-chr15:79043128..79043964,2	MCF-7	breast:
9	chr15:78292459..78292975-chr15:79043082..79043688,2	HCT-116	colon:
10	chr15:78910853..78911424-chr15:79043087..79043970,4	K562	blood:

Variant related genes	Relation type
ENSG00000238166	TF binding region
ENSG00000140395	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11856441	0.83[ASN][1000 genomes]
rs12438758	0.91[ASN][1000 genomes]
rs12439049	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12592744	0.84[ASN][1000 genomes]
rs1809415	0.88[ASN][1000 genomes]
rs2291196	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2869571	0.94[ASN][1000 genomes]
rs3743065	0.91[EUR][1000 genomes]
rs3743068	0.87[EUR][1000 genomes]
rs4887091	0.80[CEU][hapmap]
rs57224848	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58717592	0.88[ASN][1000 genomes]
rs59888683	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59934757	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62012588	0.94[ASN][1000 genomes]
rs7176492	0.85[EUR][1000 genomes]
rs7177143	0.91[EUR][1000 genomes]
rs7178741	0.84[ASN][1000 genomes]
rs7182567	0.84[CEU][hapmap]
rs8024939	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917303	chr15:78491050-79205255	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	122 gene(s)	inside rSNPs	diseases
2	nsv974606	chr15:78996783-79048337	Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv904431	chr15:79006442-79155088	Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3861181	ADAMTS7	cis	multi-tissue	Pritchard

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:79033000-79045000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:79040600-79060000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr15:79042200-79043400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr15:79042400-79043400	Weak transcription	Spleen	Spleen
5	chr15:79042800-79043400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
6	chr15:79042800-79043400	Bivalent Enhancer	Fetal Muscle Leg	muscle
7	chr15:79042800-79043400	Enhancers	Rectal Mucosa Donor 29	rectum
8	chr15:79042800-79043400	Flanking Active TSS	Stomach Smooth Muscle	stomach
9	chr15:79042800-79043800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr15:79042800-79043800	Enhancers	Liver	Liver
11	chr15:79042800-79044000	Enhancers	Brain Cingulate Gyrus	brain
12	chr15:79042800-79044000	Bivalent Enhancer	Fetal Stomach	stomach
13	chr15:79042800-79044000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
14	chr15:79042800-79045000	Enhancers	Fetal Heart	heart
15	chr15:79042800-79055400	Enhancers	Right Ventricle	heart
16	chr15:79043000-79043400	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr15:79043000-79043400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr15:79043000-79043400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
19	chr15:79043000-79043400	Flanking Active TSS	Adipose Nuclei	Adipose
20	chr15:79043000-79043400	Flanking Active TSS	Brain Hippocampus Middle	brain
21	chr15:79043000-79043400	Enhancers	Brain Inferior Temporal Lobe	brain
22	chr15:79043000-79043400	Active TSS	Brain Substantia Nigra	brain
23	chr15:79043000-79043400	Enhancers	Right Atrium	heart
24	chr15:79043000-79043400	Flanking Active TSS	Hela-S3	cervix
25	chr15:79043000-79043400	Flanking Active TSS	HSMMtube	muscle
26	chr15:79043000-79043400	Enhancers	NH-A	brain
27	chr15:79043000-79043400	Enhancers	NHLF	lung
28	chr15:79043000-79043600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr15:79043000-79043600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr15:79043000-79043600	Enhancers	Colonic Mucosa	Colon
31	chr15:79043000-79043600	Active TSS	A549	lung
32	chr15:79043000-79043600	Bivalent/Poised TSS	HepG2	liver
33	chr15:79043000-79043600	Flanking Active TSS	HSMM	muscle
34	chr15:79043000-79043800	Enhancers	Primary T helper naive cells from peripheral blood	blood
35	chr15:79043000-79043800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr15:79043000-79043800	Active TSS	Colon Smooth Muscle	Colon
37	chr15:79043000-79043800	Enhancers	Duodenum Mucosa	Duodenum
38	chr15:79043000-79043800	Enhancers	Esophagus	oesophagus
39	chr15:79043000-79043800	Enhancers	Thymus	Thymus
40	chr15:79043000-79044000	Enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr15:79043000-79044000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr15:79043000-79044000	Enhancers	Cortex derived primary cultured neurospheres	brain
43	chr15:79043000-79044000	Enhancers	Left Ventricle	heart
44	chr15:79043000-79044000	Enhancers	Stomach Mucosa	stomach
45	chr15:79043000-79044000	Enhancers	HUVEC	blood vessel
46	chr15:79043000-79044200	Enhancers	Primary B cells from peripheral blood	blood
47	chr15:79043000-79044200	Enhancers	Placenta	Placenta
48	chr15:79043000-79044400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
49	chr15:79043200-79043400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr15:79043200-79043400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell

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