Variant report

Variant	rs907594
Chromosome Location	chr15:77197745-77197746
allele	A/C
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	NFYA	chr15:77197621-77198001	Hela-S3	cervix:	n/a	n/a
2	CEBPB	chr15:77197415-77198067	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr15:77197395-77197826	GM12891	blood:	n/a	n/a
4	USF1	chr15:77197444-77197963	SK-N-SH_RA	brain:	n/a	chr15:77197760-77197776
5	POLR2A	chr15:77196737-77198240	H1-neurons	neurons:	n/a	n/a
6	CTCF	chr15:77197743-77197809	Lung_OC	lung:	n/a	n/a
7	YY1	chr15:77197029-77198030	HepG2	liver:	n/a	chr15:77197395-77197406 chr15:77197537-77197547 chr15:77197533-77197542 chr15:77197458-77197469 chr15:77197267-77197281 chr15:77197296-77197307 chr15:77197537-77197559 chr15:77197534-77197554 chr15:77197537-77197547 chr15:77197540-77197548 chr15:77197535-77197554
8	UBTF	chr15:77197065-77198215	K562	blood:	n/a	n/a
9	POLR2A	chr15:77197334-77198008	GM12878	blood:	n/a	n/a
10	BRCA1	chr15:77197617-77198266	Hela-S3	cervix:	n/a	n/a
11	CTCF	chr15:77197740-77197890	WERI-Rb-1	eye:	n/a	n/a
12	POLR2A	chr15:77196788-77198022	GM12892	blood:	n/a	n/a
13	POLR2A	chr15:77197223-77198061	GM18951	blood:	n/a	n/a
14	POLR2A	chr15:77197329-77198146	ProgFib	skin:	n/a	n/a
15	POLR2A	chr15:77197044-77198026	HepG2	liver:	n/a	n/a
16	SIN3A	chr15:77196803-77198391	H1-hESC	embryonic stem cell:	n/a	chr15:77197749-77197758
17	MAX	chr15:77196899-77198315	HCT-116	colon:	n/a	chr15:77197746-77197759 chr15:77197748-77197757 chr15:77197746-77197759 chr15:77197747-77197758 chr15:77197748-77197757 chr15:77197748-77197758
18	SP1	chr15:77197281-77198155	A549	lung:	n/a	chr15:77197510-77197519 chr15:77197506-77197520 chr15:77197460-77197469 chr15:77197969-77197983 chr15:77197478-77197487
19	SIN3AK20	chr15:77196772-77198246	MCF-7	breast:	n/a	n/a
20	MAX	chr15:77197617-77198341	H1-hESC	embryonic stem cell:	n/a	chr15:77197746-77197759 chr15:77197748-77197757 chr15:77197746-77197759 chr15:77197747-77197758 chr15:77197748-77197757 chr15:77197748-77197758
21	FOXA1	chr15:77197485-77197966	HepG2	liver:	n/a	n/a
22	POLR2A	chr15:77196960-77198019	GM18526	blood:	n/a	n/a
23	E2F6	chr15:77197606-77198136	K562	blood:	n/a	chr15:77197806-77197815 chr15:77197762-77197777 chr15:77197842-77197853
24	POLR2A	chr15:77197230-77197973	GM12878	blood:	n/a	n/a
25	JUND	chr15:77197512-77198151	K562	blood:	n/a	n/a
26	POLR2A	chr15:77197172-77198288	SK-N-MC	brain:	n/a	n/a
27	YY1	chr15:77196796-77197889	H1-hESC	embryonic stem cell:	n/a	chr15:77197395-77197406 chr15:77197537-77197547 chr15:77197533-77197542 chr15:77197458-77197469 chr15:77197267-77197281 chr15:77197296-77197307 chr15:77197537-77197559 chr15:77197534-77197554 chr15:77197537-77197547 chr15:77197540-77197548 chr15:77197535-77197554
28	TAF1	chr15:77197403-77197825	GM12878	blood:	n/a	n/a
29	POLR2A	chr15:77197373-77197880	GM12891	blood:	n/a	n/a
30	POLR2A	chr15:77197211-77197965	HUVEC	blood vessel:	n/a	n/a
31	ZEB1	chr15:77196757-77197834	GM12878	blood:	n/a	chr15:77197504-77197511
32	FOXP2	chr15:77197577-77197950	SK-N-MC	brain:	n/a	n/a
33	POLR2A	chr15:77196766-77198218	H1-neurons	neurons:	n/a	n/a
34	CTCF	chr15:77197660-77197810	GM12872	blood:	n/a	n/a
35	MBD4	chr15:77197609-77198184	HepG2	liver:	n/a	n/a
36	CHD2	chr15:77197419-77198049	GM12878	blood:	n/a	chr15:77197844-77197854
37	MAX	chr15:77196768-77198565	HepG2	liver:	n/a	chr15:77197746-77197759 chr15:77197748-77197757 chr15:77197746-77197759 chr15:77197747-77197758 chr15:77197748-77197757 chr15:77197748-77197758
38	POLR2A	chr15:77197387-77198066	HEK293	kidney:	n/a	n/a
39	MYC	chr15:77197609-77197882	MCF10A-Er-Src	breast:	n/a	chr15:77197746-77197759 chr15:77197748-77197757 chr15:77197746-77197759 chr15:77197747-77197758 chr15:77197748-77197757 chr15:77197748-77197758
40	E2F6	chr15:77196880-77198203	Hela-S3	cervix:	n/a	chr15:77196974-77196985 chr15:77197806-77197815 chr15:77197533-77197542 chr15:77196974-77196985 chr15:77197762-77197777 chr15:77196974-77196981 chr15:77197842-77197853
41	POLR2A	chr15:77197395-77197986	H1-hESC	embryonic stem cell:	n/a	n/a
42	YY1	chr15:77197097-77197919	SK-N-SH_RA	brain:	n/a	chr15:77197395-77197406 chr15:77197537-77197547 chr15:77197533-77197542 chr15:77197458-77197469 chr15:77197267-77197281 chr15:77197296-77197307 chr15:77197537-77197559 chr15:77197534-77197554 chr15:77197537-77197547 chr15:77197540-77197548 chr15:77197535-77197554
43	TAF1	chr15:77197411-77197992	Hela-S3	cervix:	n/a	n/a
44	MXI1	chr15:77196758-77197962	Hela-S3	cervix:	n/a	chr15:77197749-77197758
45	ZNF143	chr15:77197644-77198006	Hela-S3	cervix:	n/a	n/a
46	YY1	chr15:77197400-77197865	A549	lung:	n/a	chr15:77197537-77197547 chr15:77197533-77197542 chr15:77197458-77197469 chr15:77197537-77197559 chr15:77197534-77197554 chr15:77197537-77197547 chr15:77197540-77197548 chr15:77197535-77197554
47	UBTF	chr15:77197603-77197944	K562	blood:	n/a	n/a
48	POLR2A	chr15:77197273-77198130	HUVEC	blood vessel:	n/a	n/a
49	USF1	chr15:77197436-77198097	SK-N-SH	brain:	n/a	chr15:77197760-77197776
50	ATF3	chr15:77197466-77197969	H1-hESC	embryonic stem cell:	n/a	chr15:77197880-77197889 chr15:77197578-77197587

No.	Distal block	Cell Line	Cell type
1	chr15:77196909..77199186-chr15:77360659..77363469,2	K562	blood:
2	chr15:77196194..77198493-chr15:77235491..77237833,2	K562	blood:
3	chr15:77195708..77198409-chr15:77360659..77363583,2	K562	blood:
4	chr15:77196272..77198559-chr15:77223364..77225357,2	K562	blood:
5	chr15:77196182..77198169-chr15:77222869..77226186,3	K562	blood:
6	chr15:77195051..77197848-chr15:77221697..77224553,2	MCF-7	breast:
7	chr15:77194744..77199863-chr15:77220881..77225601,7	MCF-7	breast:

Variant related genes	Relation type
SCAPER	TF binding region
ENSG00000140391	Chromatin interaction
ENSG00000117906	Chromatin interaction
ENSG00000269951	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10851892	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11072636	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11072637	0.86[ASN][1000 genomes]
rs11635584	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11637296	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12050866	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12903331	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12903586	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12909065	0.81[AMR][1000 genomes]
rs1567671	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2280194	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2404600	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34450864	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35940181	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3812908	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3812909	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4886506	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4886840	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4886842	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55817928	0.81[ASN][1000 genomes]
rs56275930	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6495224	0.83[ASN][1000 genomes]
rs907593	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9707794	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3440794	chr15:76764595-77571114	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3367577	chr15:77015618-77442634	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	esv1803942	chr15:77151005-77210457	Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv1040852	chr15:77160237-78137541	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
5	esv2758388	chr15:77170550-77373448	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	esv2760041	chr15:77170550-77373448	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs907594	SCAPER	cis	lung	GTEx
rs907594	SCAPER	cis	Nerve Tibial	GTEx
rs907594	SCAPER	cis	Esophagus Mucosa	GTEx
rs907594	SCAPER	cis	Esophagus Muscularis	GTEx
rs907594	SCAPER	cis	Artery Tibial	GTEx
rs907594	SCAPER	Cis_1M	lymphoblastoid	RTeQTL
rs907594	SCAPER	cis	Thyroid	GTEx
rs907594	SCAPER	cis	Adipose Subcutaneous	GTEx
rs907594	ISL2	Cis_1M	lymphoblastoid	RTeQTL
rs907594	SCAPER	cis	Whole Blood	GTEx
rs907594	SCAPER	cis	Skin Sun Exposed Lower leg	GTEx
rs907594	SCAPER	cis	Stomach	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77195400-77198600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr15:77196200-77198200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr15:77196400-77197800	Active TSS	Fetal Brain Male	brain
4	chr15:77196400-77198000	Active TSS	Stomach Smooth Muscle	stomach
5	chr15:77196400-77198200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr15:77196400-77198200	Active TSS	Brain Inferior Temporal Lobe	brain
7	chr15:77196600-77198000	Active TSS	Fetal Intestine Small	intestine
8	chr15:77196600-77198000	Active TSS	Fetal Stomach	stomach
9	chr15:77196600-77198200	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr15:77196600-77198200	Active TSS	Brain Substantia Nigra	brain
11	chr15:77196600-77198400	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr15:77196800-77197800	Active TSS	Pancreas	Pancrea
13	chr15:77196800-77197800	Active TSS	Osteobl	bone
14	chr15:77196800-77198000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr15:77196800-77198000	Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr15:77196800-77198000	Active TSS	iPS-15b Cell Line	embryonic stem cell
17	chr15:77196800-77198000	Active TSS	Left Ventricle	heart
18	chr15:77196800-77198000	Active TSS	Lung	lung
19	chr15:77196800-77198000	Active TSS	Rectal Smooth Muscle	rectum
20	chr15:77196800-77198000	Active TSS	NHDF-Ad	bronchial
21	chr15:77196800-77198200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
22	chr15:77196800-77198200	Active TSS	H9 Cell Line	embryonic stem cell
23	chr15:77196800-77198200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr15:77196800-77198200	Active TSS	Duodenum Smooth Muscle	Duodenum
25	chr15:77196800-77198400	Active TSS	Fetal Kidney	kidney
26	chr15:77196800-77198400	Active TSS	Ovary	ovary
27	chr15:77196800-77198600	Active TSS	Aorta	Aorta
28	chr15:77196800-77198800	Flanking Active TSS	Primary hematopoietic stem cells	blood
29	chr15:77197000-77197800	Active TSS	Small Intestine	intestine
30	chr15:77197000-77198000	Active TSS	H1 Cell Line	embryonic stem cell
31	chr15:77197000-77198000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr15:77197000-77198000	Active TSS	Primary T helper naive cells from peripheral blood	blood
33	chr15:77197000-77198000	Active TSS	Primary T killer memory cells from peripheral blood	blood
34	chr15:77197000-77198000	Active TSS	Brain Angular Gyrus	brain
35	chr15:77197000-77198000	Active TSS	Brain Cingulate Gyrus	brain
36	chr15:77197000-77198000	Active TSS	Brain Hippocampus Middle	brain
37	chr15:77197000-77198000	Active TSS	Colon Smooth Muscle	Colon
38	chr15:77197000-77198000	Active TSS	Fetal Intestine Large	intestine
39	chr15:77197000-77198000	Active TSS	Gastric	stomach
40	chr15:77197000-77198000	Active TSS	Sigmoid Colon	Sigmoid Colon
41	chr15:77197000-77198000	Active TSS	A549	lung
42	chr15:77197000-77198000	Active TSS	HSMMtube	muscle
43	chr15:77197000-77198200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr15:77197000-77198200	Active TSS	iPS-20b Cell Line	embryonic stem cell
45	chr15:77197000-77198200	Active TSS	Fetal Brain Female	brain
46	chr15:77197000-77198200	Active TSS	Psoas Muscle	Psoas
47	chr15:77197200-77197800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr15:77197200-77197800	Active TSS	HUES6 Cell Line	embryonic stem cell
49	chr15:77197200-77197800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr15:77197200-77197800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell

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