Variant report

Variant	rs16957715
Chromosome Location	chr15:43708737-43708738
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	POLR2A	chr15:43708577-43708741	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:43703560..43705844-chr15:43707293..43708833,2	K562	blood:
2	chr15:43398098..43400146-chr15:43707936..43709689,2	K562	blood:
3	chr15:43706104..43709030-chr15:43712265..43715613,5	K562	blood:
4	chr15:43706323..43709082-chr15:43711467..43715613,3	K562	blood:

Variant related genes	Relation type
TP53BP1	TF binding region
ENSG00000067369	Chromatin interaction
ENSG00000159459	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10518812	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[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]
rs1095386	0.94[YRI][hapmap]
rs12899865	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12900259	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12905220	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12906017	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12906481	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12907870	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12908460	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12911569	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12911740	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];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12912744	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap];0.94[YRI][hapmap]
rs12913977	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12914122	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16957680	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16957730	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17723479	0.95[CEU][hapmap];0.94[YRI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17780417	1.00[CEU][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17780920	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]
rs1814324	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1814538	1.00[YRI][hapmap]
rs2230451	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2242069	0.80[LWK][hapmap];1.00[YRI][hapmap]
rs2264876	0.80[LWK][hapmap];1.00[YRI][hapmap]
rs2439832	0.80[LWK][hapmap];1.00[YRI][hapmap]
rs2439850	1.00[YRI][hapmap]
rs2444032	1.00[YRI][hapmap]
rs2444250	1.00[YRI][hapmap]
rs2467736	1.00[YRI][hapmap]
rs2467739	0.80[LWK][hapmap];1.00[YRI][hapmap]
rs34002293	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34178146	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34181131	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34212866	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34388946	0.81[EUR][1000 genomes]
rs34515241	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34591748	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34633582	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34657657	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34661349	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34697113	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34715468	0.85[AMR][1000 genomes]
rs34767197	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34860428	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34921640	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35158584	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35160541	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35278805	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35311230	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs35326382	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35681736	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35903301	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35958032	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35975365	0.86[EUR][1000 genomes]
rs35992154	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs36078097	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3862138	0.83[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap];0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs495175	1.00[YRI][hapmap]
rs514438	1.00[CEU][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs537115	0.80[LWK][hapmap];1.00[YRI][hapmap]
rs55748552	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55801120	0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs57728767	0.96[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs60018990	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs60367691	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs62019432	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62019442	0.81[AMR][1000 genomes]
rs62020574	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62020575	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62020612	0.81[EUR][1000 genomes]
rs62020616	0.81[EUR][1000 genomes]
rs62021176	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62021180	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs66629206	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs689647	1.00[YRI][hapmap]
rs689781	1.00[YRI][hapmap]
rs689826	1.00[YRI][hapmap]
rs689835	1.00[YRI][hapmap]
rs690316	1.00[YRI][hapmap]
rs690466	1.00[YRI][hapmap]
rs7048	0.90[ASW][hapmap];0.81[GIH][hapmap]
rs71476435	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7168220	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7173383	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7176923	0.95[CEU][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7177146	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.96[TSI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7177892	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7180812	0.90[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.96[TSI][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7181545	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7181634	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[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]
rs7181783	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7182292	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7183708	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72707530	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72709850	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72709879	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8027748	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[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:12)

SNP	Gene	Cis/trans	Tissue	Source
rs16957715	ZSCAN29	cis	lymphoblastoid	seeQTL
rs16957715	ZFP106	cis	cerebellum	SCAN
rs16957715	ZSCAN29	cis	multi-tissue	Pritchard
rs16957715	FLJ35867	cis	multi-tissue	Pritchard
rs16957715	TUBGCP4	cis	cerebellum	SCAN
rs16957715	DUOXA1	cis	parietal	SCAN
rs16957715	TUBGCP4	cis	Artery Tibial	GTEx
rs16957715	TGM7	cis	Esophagus Mucosa	GTEx
rs16957715	ADAL	cis	cerebellum	SCAN
rs16957715	LCMT2	cis	Esophagus Mucosa	GTEx
rs16957715	ZNF690	cis	multi-tissue	Pritchard
rs16957715	ZSCAN29	cis	Esophagus Muscularis	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43665000-43730000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:43668000-43717800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr15:43668200-43732800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr15:43675600-43744400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr15:43682800-43720800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr15:43682800-43727800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr15:43683200-43709000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr15:43683400-43732200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
9	chr15:43684800-43709000	Strong transcription	Dnd41	blood
10	chr15:43685000-43709000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr15:43685000-43709000	Strong transcription	Left Ventricle	heart
12	chr15:43685000-43720400	Strong transcription	Fetal Brain Female	brain
13	chr15:43685800-43710200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr15:43686000-43717200	Strong transcription	Primary B cells from cord blood	blood
15	chr15:43686000-43717200	Strong transcription	Fetal Lung	lung
16	chr15:43686000-43720600	Strong transcription	Brain Germinal Matrix	brain
17	chr15:43686000-43727000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr15:43686400-43709200	Strong transcription	Fetal Thymus	thymus
19	chr15:43686400-43710000	Strong transcription	H1 Cell Line	embryonic stem cell
20	chr15:43686400-43711200	Strong transcription	Rectal Mucosa Donor 31	rectum
21	chr15:43686400-43715400	Strong transcription	Fetal Intestine Large	intestine
22	chr15:43686600-43708800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr15:43686600-43709200	Strong transcription	Primary T cells fromperipheralblood	blood
24	chr15:43686600-43715800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr15:43686600-43720400	Strong transcription	Fetal Muscle Trunk	muscle
26	chr15:43686600-43720400	Strong transcription	Fetal Muscle Leg	muscle
27	chr15:43686600-43726000	Strong transcription	Primary B cells from peripheral blood	blood
28	chr15:43686600-43733200	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr15:43686600-43733800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr15:43686800-43708800	Strong transcription	Sigmoid Colon	Sigmoid Colon
31	chr15:43686800-43709200	Strong transcription	NH-A	brain
32	chr15:43686800-43710000	Strong transcription	Primary hematopoietic stem cells	blood
33	chr15:43686800-43710000	Strong transcription	Primary T helper cells PMA-I stimulated	--
34	chr15:43686800-43710000	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr15:43686800-43710200	Strong transcription	Placenta	Placenta
36	chr15:43686800-43717800	Strong transcription	Primary T cells from cord blood	blood
37	chr15:43686800-43725400	Strong transcription	Skeletal Muscle Female	skeletal muscle
38	chr15:43686800-43725600	Strong transcription	Osteobl	bone
39	chr15:43686800-43733400	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr15:43687000-43725400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr15:43687000-43732200	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr15:43687200-43733400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
43	chr15:43687400-43709000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr15:43687600-43731600	Strong transcription	Cortex derived primary cultured neurospheres	brain
45	chr15:43689200-43737200	Weak transcription	Stomach Mucosa	stomach
46	chr15:43693400-43708800	Strong transcription	Brain Cingulate Gyrus	brain
47	chr15:43693400-43714200	Strong transcription	Hela-S3	cervix
48	chr15:43693800-43710000	Strong transcription	NHDF-Ad	bronchial
49	chr15:43694400-43709800	Strong transcription	HSMM	muscle
50	chr15:43694800-43710200	Strong transcription	Brain Anterior Caudate	brain

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