Variant report

Variant	rs2945972
Chromosome Location	chr19:36870628-36870629
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	POLR2A	chr19:36869453-36870641	PFSK-1	brain:	n/a	n/a
2	GATA3	chr19:36869183-36870654	A549	lung:	n/a	chr19:36869509-36869519 chr19:36869673-36869684
3	TCF12	chr19:36869282-36870764	A549	lung:	n/a	chr19:36869685-36869693
4	MAX	chr19:36869266-36870848	A549	lung:	n/a	chr19:36869774-36869783 chr19:36869415-36869424
5	E2F6	chr19:36869421-36870759	A549	lung:	n/a	chr19:36870213-36870225 chr19:36870179-36870188 chr19:36870214-36870225
6	KAP1	chr19:36869437-36870652	HEK293	kidney:	n/a	n/a
7	GATA2	chr19:36868970-36870641	SH-SY5Y	brain:	n/a	chr19:36869509-36869519 chr19:36869673-36869684
8	POLR2A	chr19:36869506-36871026	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:36869355..36872280-chr19:37261242..37264152,2	MCF-7	breast:
2	chr19:36869703..36871321-chr19:37018127..37020542,2	K562	blood:
3	chr19:36868756..36870628-chr19:37018916..37021157,2	MCF-7	breast:

Variant related genes	Relation type
ZFP14	TF binding region
ENSG00000228629	Chromatin interaction
ENSG00000267260	Chromatin interaction
ENSG00000267041	Chromatin interaction
ENSG00000254004	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10402043	0.82[GIH][hapmap]
rs10402405	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10404574	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10409091	0.95[CHB][hapmap]
rs10414054	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10418510	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10420071	0.86[ASW][hapmap];0.81[CHB][hapmap];0.82[GIH][hapmap];0.88[LWK][hapmap];0.88[MKK][hapmap]
rs10420610	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10426014	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10439091	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12459465	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12971694	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12976881	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2070132	0.90[CHB][hapmap];0.91[CHD][hapmap];0.90[MEX][hapmap];0.80[TSI][hapmap]
rs2271844	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2287897	0.95[CHB][hapmap];0.91[MEX][hapmap];0.80[TSI][hapmap]
rs2287898	0.95[CHB][hapmap];0.91[MEX][hapmap];0.80[TSI][hapmap]
rs2385799	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2385800	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2385801	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2385803	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2385804	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs2385805	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2432039	0.90[CHB][hapmap]
rs2432045	0.90[CHB][hapmap];0.83[CHD][hapmap];0.91[MEX][hapmap];0.80[TSI][hapmap]
rs2432049	0.90[CHB][hapmap]
rs2432054	0.90[CHB][hapmap];0.95[CHD][hapmap];0.91[MEX][hapmap];0.80[TSI][hapmap]
rs2438514	0.90[CHB][hapmap];0.95[CHD][hapmap];0.90[MEX][hapmap];0.80[TSI][hapmap]
rs2438517	0.90[CHB][hapmap];0.95[CHD][hapmap];0.91[MEX][hapmap];0.80[TSI][hapmap]
rs2918349	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2945945	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2945948	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2945949	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2945950	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2945951	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2945957	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2945961	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][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];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2945963	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2945971	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2945985	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap]
rs2945992	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2945993	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2945994	0.90[ASN][1000 genomes]
rs2945995	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2967484	1.00[ASW][hapmap];0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2967493	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2967496	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2967501	0.87[AFR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2967504	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2967506	0.87[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2967509	0.99[ASN][1000 genomes]
rs2967510	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2967512	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2967515	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2967517	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2967518	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2967521	0.93[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2967523	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2967524	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2967526	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2967543	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2972632	0.81[ASN][1000 genomes]
rs2972633	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4006082	0.82[ASN][1000 genomes]
rs4239585	0.90[CHB][hapmap]
rs4806321	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5021030	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58703752	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62112565	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6417185	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6510541	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6510542	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7246106	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7251979	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7255260	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7255403	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8102020	0.95[CHB][hapmap];0.91[MEX][hapmap];0.80[TSI][hapmap]
rs8106095	0.85[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs8109320	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8109333	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8112312	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8182628	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833816	chr19:36824257-37034287	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2945972	ZNF527	cis	cerebellum	SCAN
rs2945972	LINC00665	cis	Muscle Skeletal	GTEx
rs2945972	LOC284412	N/A	lymphoblastoid	RTeQTL
rs2945972	TMEM91	cis	cerebellum	SCAN

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36868600-36870800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr19:36868800-36870800	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr19:36869000-36870800	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr19:36869000-36870800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr19:36869200-36870800	Active TSS	H9 Cell Line	embryonic stem cell
6	chr19:36869200-36870800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr19:36869200-36870800	Active TSS	Brain Angular Gyrus	brain
8	chr19:36869200-36870800	Active TSS	Fetal Kidney	kidney
9	chr19:36869200-36870800	Active TSS	Psoas Muscle	Psoas
10	chr19:36869200-36871200	Active TSS	HSMM	muscle
11	chr19:36869400-36870800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr19:36869400-36870800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr19:36869400-36870800	Active TSS	Muscle Satellite Cultured Cells	--
14	chr19:36869400-36870800	Active TSS	Brain Anterior Caudate	brain
15	chr19:36869400-36870800	Active TSS	Brain Substantia Nigra	brain
16	chr19:36869400-36870800	Active TSS	Duodenum Smooth Muscle	Duodenum
17	chr19:36869400-36870800	Active TSS	Fetal Lung	lung
18	chr19:36869400-36870800	Active TSS	Rectal Mucosa Donor 31	rectum
19	chr19:36869400-36870800	Active TSS	Rectal Smooth Muscle	rectum
20	chr19:36869400-36870800	Active TSS	Hela-S3	cervix
21	chr19:36869400-36870800	Active TSS	NHEK	skin
22	chr19:36869400-36870800	Active TSS	Osteobl	bone
23	chr19:36869600-36870800	Active TSS	Primary T killer memory cells from peripheral blood	blood
24	chr19:36869600-36870800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr19:36869600-36870800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
26	chr19:36869600-36870800	Active TSS	Duodenum Mucosa	Duodenum
27	chr19:36869800-36870800	Active TSS	Stomach Smooth Muscle	stomach
28	chr19:36869800-36870800	Active TSS	Monocytes-CD14+_RO01746	blood
29	chr19:36870200-36870800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
30	chr19:36870200-36870800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr19:36870200-36870800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
32	chr19:36870200-36870800	ZNF genes & repeats	Fetal Thymus	thymus
33	chr19:36870200-36870800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
34	chr19:36870200-36870800	Flanking Active TSS	Dnd41	blood
35	chr19:36870200-36871000	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
36	chr19:36870200-36871000	ZNF genes & repeats	Fetal Stomach	stomach
37	chr19:36870400-36870800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr19:36870400-36870800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr19:36870400-36870800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
40	chr19:36870400-36870800	ZNF genes & repeats	Colon Smooth Muscle	Colon
41	chr19:36870400-36870800	Flanking Active TSS	Fetal Brain Male	brain
42	chr19:36870400-36870800	ZNF genes & repeats	Fetal Intestine Small	intestine
43	chr19:36870400-36870800	Flanking Active TSS	Pancreas	Pancrea
44	chr19:36870400-36870800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
45	chr19:36870400-36871000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
46	chr19:36870400-36871000	ZNF genes & repeats	A549	lung
47	chr19:36870600-36870800	Enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr19:36870600-36870800	Active TSS	Primary B cells from cord blood	blood
49	chr19:36870600-36870800	Enhancers	Primary B cells from peripheral blood	blood
50	chr19:36870600-36870800	Enhancers	Primary T cells from cord blood	blood

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