Variant report

Variant	rs17780920
Chromosome Location	chr15:43662362-43662363
allele	C/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	MAX	chr15:43662087-43664177	K562	blood:	n/a	chr15:43664002-43664012 chr15:43663667-43663677 chr15:43662637-43662647 chr15:43662682-43662690
2	CTCF	chr15:43662260-43662410	GM12868	blood:	n/a	n/a
3	POLR2A	chr15:43662183-43664059	HepG2	liver:	n/a	n/a
4	REST	chr15:43662245-43662866	PFSK-1	brain:	n/a	n/a
5	SIN3A	chr15:43662124-43664379	H1-hESC	embryonic stem cell:	n/a	chr15:43662912-43662921 chr15:43663392-43663403 chr15:43663686-43663695
6	MAX	chr15:43662144-43664194	NB4	blood:	n/a	chr15:43664002-43664012 chr15:43663667-43663677 chr15:43662637-43662647 chr15:43662682-43662690
7	MXI1	chr15:43661956-43664627	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr15:43662059-43664009	GM12891	blood:	n/a	n/a
9	REST	chr15:43662269-43663066	HL-60	blood:	n/a	chr15:43662944-43662962
10	REST	chr15:43662333-43664003	K562	blood:	n/a	chr15:43662944-43662962 chr15:43663330-43663348
11	POLR2A	chr15:43662055-43663767	SK-N-MC	brain:	n/a	n/a
12	ZNF263	chr15:43662310-43663948	HEK293-T-REx	kidney:	n/a	n/a
13	HCFC1	chr15:43661352-43665311	Hela-S3	cervix:	n/a	n/a
14	REST	chr15:43662304-43662945	PFSK-1	brain:	n/a	n/a
15	CTCF	chr15:43662240-43662390	GM12864	blood:	n/a	n/a
16	POLR2A	chr15:43662344-43664040	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr15:43662019-43664130	MCF10A-Er-Src	breast:	n/a	n/a
18	POLR2A	chr15:43662087-43663828	MCF10A-Er-Src	breast:	n/a	n/a
19	CHD2	chr15:43662356-43662681	K562	blood:	n/a	chr15:43662634-43662644
20	REST	chr15:43662252-43662834	H1-hESC	embryonic stem cell:	n/a	n/a
21	SIN3AK20	chr15:43662353-43662950	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr15:43662296-43663492	K562	blood:	n/a	n/a
23	REST	chr15:43662307-43662811	SK-N-SH	brain:	n/a	n/a
24	POLR2A	chr15:43661060-43663929	Hela-S3	cervix:	n/a	n/a
25	SIN3AK20	chr15:43662349-43664140	K562	blood:	n/a	n/a
26	REST	chr15:43662310-43662781	Hela-S3	cervix:	n/a	n/a
27	REST	chr15:43662346-43662680	MCF-7	breast:	n/a	n/a
28	GTF2F1	chr15:43662350-43662482	Hela-S3	cervix:	n/a	n/a
29	CTCF	chr15:43662300-43662450	GM12873	blood:	n/a	n/a
30	CTCF	chr15:43662220-43662370	GM12874	blood:	n/a	n/a
31	MYC	chr15:43662279-43664156	K562	blood:	n/a	chr15:43664002-43664012 chr15:43663667-43663677 chr15:43662637-43662647 chr15:43662682-43662690

No.	Distal block	Cell Line	Cell type
1	chr15:43661645..43664142-chr15:43669573..43672436,3	MCF-7	breast:
2	chr15:43621444..43623700-chr15:43661759..43663409,2	MCF-7	breast:
3	chr15:43660016..43662796-chr15:43702586..43705983,3	K562	blood:
4	chr15:43618581..43624264-chr15:43661265..43664929,7	MCF-7	breast:
5	chr15:43620486..43624109-chr15:43661175..43665421,4	K562	blood:
6	chr15:43619535..43624096-chr15:43662038..43665421,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TP53BP1-4	chr15:43662196-43662546	NONHSAT042069

Variant related genes	Relation type
TUBGCP4	TF binding region
ZSCAN29	TF binding region
ENSG00000137822	Chromatin interaction
ENSG00000168806	Chromatin interaction
ENSG00000168803	Chromatin interaction
ENSG00000067369	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10518812	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1095386	1.00[YRI][hapmap]
rs12899865	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12900259	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12905220	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12906017	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12906481	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12907870	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12908460	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12911569	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12911740	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12912744	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs12913977	1.00[CEU][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12914122	1.00[CEU][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16957680	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16957715	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16957730	1.00[CEU][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17723479	0.95[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17780417	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1814324	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1814538	0.94[YRI][hapmap]
rs2230451	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2242069	0.94[YRI][hapmap]
rs2264876	0.94[YRI][hapmap]
rs2439832	0.94[YRI][hapmap]
rs2439850	0.94[YRI][hapmap]
rs2444032	0.94[YRI][hapmap]
rs2444250	0.94[YRI][hapmap]
rs2467736	0.94[YRI][hapmap]
rs2467739	0.94[YRI][hapmap]
rs34002293	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34178146	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34181131	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34212866	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34515241	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34591748	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34633582	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34657657	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34661349	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34697113	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34715468	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs34767197	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34860428	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34921640	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35158584	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35160541	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35278805	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35311230	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35326382	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35681736	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35903301	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35958032	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35975365	0.93[EUR][1000 genomes]
rs35992154	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36078097	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3862138	0.95[CEU][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];0.90[MEX][hapmap]
rs495175	0.94[YRI][hapmap]
rs514438	1.00[CEU][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs537115	0.94[YRI][hapmap]
rs55748552	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55801120	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs57728767	0.83[AFR][1000 genomes]
rs60018990	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62019432	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62019442	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62020574	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62020575	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62021176	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62021180	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs66629206	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs689647	0.94[YRI][hapmap]
rs689781	0.94[YRI][hapmap]
rs689826	0.94[YRI][hapmap]
rs689835	0.94[YRI][hapmap]
rs690316	0.94[YRI][hapmap]
rs690466	0.94[YRI][hapmap]
rs7048	0.82[ASW][hapmap];0.81[GIH][hapmap];0.82[LWK][hapmap];0.85[MKK][hapmap]
rs71476435	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7168220	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7173383	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7176923	0.95[CEU][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7177146	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7177892	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7180812	0.82[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7181545	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7181634	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7181783	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7182292	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7183708	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72707530	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72709850	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72709879	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs8027748	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534649	chr15:43591116-43851142	Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	esv1846172	chr15:43632138-44116986	Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Flanking Active TSS 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 miRNA target site	101 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs17780920	WDR76	cis	parietal	SCAN
rs17780920	ZNF690	cis	multi-tissue	Pritchard
rs17780920	LCMT2	cis	Esophagus Mucosa	GTEx
rs17780920	ZSCAN29	cis	multi-tissue	Pritchard
rs17780920	ZSCAN29	cis	lymphoblastoid	seeQTL
rs17780920	TGM7	cis	Esophagus Mucosa	GTEx
rs17780920	ADAL	cis	cerebellum	SCAN
rs17780920	DUOXA1	cis	parietal	SCAN
rs17780920	TUBGCP4	cis	Artery Tibial	GTEx
rs17780920	ZSCAN29	cis	Esophagus Muscularis	GTEx
rs17780920	TUBGCP4	cis	cerebellum	SCAN
rs17780920	ZFP106	cis	cerebellum	SCAN
rs17780920	FLJ35867	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43661000-43662400	Enhancers	Primary B cells from peripheral blood	blood
2	chr15:43661000-43662400	Enhancers	Lung	lung
3	chr15:43661000-43662400	Flanking Active TSS	Stomach Smooth Muscle	stomach
4	chr15:43661000-43662600	Enhancers	Spleen	Spleen
5	chr15:43661000-43662600	Flanking Active TSS	GM12878-XiMat	blood
6	chr15:43661000-43662800	Flanking Active TSS	Dnd41	blood
7	chr15:43661000-43662800	Flanking Active TSS	Hela-S3	cervix
8	chr15:43661200-43662400	Enhancers	Primary T cells fromperipheralblood	blood
9	chr15:43661200-43662400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr15:43661200-43662400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr15:43661400-43662400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr15:43661400-43662400	Flanking Active TSS	HepG2	liver
13	chr15:43661400-43664800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr15:43661600-43662400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr15:43661600-43662400	Flanking Active TSS	Brain Germinal Matrix	brain
16	chr15:43661600-43662400	Flanking Active TSS	Fetal Brain Male	brain
17	chr15:43661600-43662400	Enhancers	Placenta Amnion	Placenta Amnion
18	chr15:43661600-43662600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr15:43661600-43662600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr15:43661600-43662600	Flanking Active TSS	Fetal Brain Female	brain
21	chr15:43661600-43662800	Flanking Active TSS	Brain Hippocampus Middle	brain
22	chr15:43661600-43662800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
23	chr15:43661600-43662800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
24	chr15:43661600-43663000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
25	chr15:43661800-43662400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
26	chr15:43661800-43662400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
27	chr15:43661800-43662400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr15:43661800-43662400	Flanking Active TSS	Fetal Heart	heart
29	chr15:43661800-43662400	Flanking Active TSS	Psoas Muscle	Psoas
30	chr15:43661800-43662400	Flanking Active TSS	NHDF-Ad	bronchial
31	chr15:43661800-43662600	Flanking Active TSS	H1 Cell Line	embryonic stem cell
32	chr15:43661800-43662600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
33	chr15:43661800-43662600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr15:43661800-43662600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
35	chr15:43661800-43662600	Flanking Active TSS	Right Ventricle	heart
36	chr15:43661800-43662800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr15:43661800-43662800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
38	chr15:43661800-43662800	Flanking Active TSS	Adipose Nuclei	Adipose
39	chr15:43661800-43662800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
40	chr15:43661800-43662800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
41	chr15:43661800-43662800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
42	chr15:43661800-43663000	Flanking Active TSS	Primary hematopoietic stem cells	blood
43	chr15:43661800-43663000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
44	chr15:43661800-43663000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr15:43661800-43663800	Active TSS	NHLF	lung
46	chr15:43661800-43664000	Active TSS	iPS-15b Cell Line	embryonic stem cell
47	chr15:43661800-43664000	Active TSS	HSMM	muscle
48	chr15:43662000-43662400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
49	chr15:43662000-43662400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr15:43662000-43662400	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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