Variant report

Variant	rs2945948
Chromosome Location	chr19:36912559-36912560
allele	A/G
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	E2F6	chr19:36912266-36913072	H1-hESC	embryonic stem cell:	n/a	chr19:36912697-36912704 chr19:36912616-36912630 chr19:36912470-36912480 chr19:36912693-36912707
2	POLR2A	chr19:36912400-36912887	MCF-7	breast:	n/a	n/a
3	MAX	chr19:36912319-36912995	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr19:36912232-36912759	HUVEC	blood vessel:	n/a	n/a
5	NRF1	chr19:36912303-36912828	SK-N-SH	brain:	n/a	chr19:36912536-36912550
6	RAD21	chr19:36912191-36912615	H1-hESC	embryonic stem cell:	n/a	chr19:36912335-36912354 chr19:36912340-36912350
7	E2F6	chr19:36912220-36913022	H1-hESC	embryonic stem cell:	n/a	chr19:36912697-36912704 chr19:36912616-36912630 chr19:36912470-36912480 chr19:36912693-36912707
8	POLR2A	chr19:36912500-36912903	MCF-7	breast:	n/a	n/a
9	MAX	chr19:36912292-36913041	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
ZFP82	TF binding region

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10402405	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10404574	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10414054	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10418510	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10420610	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10426014	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10439091	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12459465	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12971694	0.85[EUR][1000 genomes]
rs12976881	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2271844	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2385799	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2385800	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2385801	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2385803	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2385805	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2945945	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2945949	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2945950	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2945951	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2945957	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2945961	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2945963	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2945971	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2945972	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2945992	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2945993	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2945995	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2967501	0.81[AFR][1000 genomes]
rs2967504	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2967510	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2967512	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2967515	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2967517	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2967518	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2967521	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2967523	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2967524	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2967525	0.82[ASN][1000 genomes]
rs2967526	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2967543	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2972633	0.80[AFR][1000 genomes]
rs5021030	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58703752	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6417185	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6510541	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs6510542	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7246106	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7251979	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7255260	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7255403	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8109320	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8109333	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8112312	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8182628	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
2	nsv1066026	chr19:36878441-36947928	ZNF genes & repeats Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
3	nsv1067101	chr19:36901010-36956251	ZNF genes & repeats Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv1064851	chr19:36910259-37689721	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2945948	LINC00665	cis	Muscle Skeletal	GTEx
rs2945948	LOC284412	N/A	lymphoblastoid	RTeQTL

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36911400-36913200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
2	chr19:36911400-36913400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
3	chr19:36911600-36912800	Bivalent/Poised TSS	Primary B cells from cord blood	blood
4	chr19:36911800-36913400	Active TSS	Brain Inferior Temporal Lobe	brain
5	chr19:36911800-36913600	Bivalent/Poised TSS	Primary T cells from cord blood	blood
6	chr19:36912000-36912600	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr19:36912000-36912600	Weak transcription	Fetal Heart	heart
8	chr19:36912000-36912600	Active TSS	Right Ventricle	heart
9	chr19:36912000-36912800	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr19:36912000-36912800	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
11	chr19:36912000-36912800	Active TSS	Right Atrium	heart
12	chr19:36912000-36913000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
13	chr19:36912000-36913000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
14	chr19:36912000-36913000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
15	chr19:36912000-36913000	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
16	chr19:36912000-36913000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr19:36912000-36913000	Bivalent/Poised TSS	Brain Germinal Matrix	brain
18	chr19:36912000-36913000	Active TSS	Brain Hippocampus Middle	brain
19	chr19:36912000-36913000	Bivalent/Poised TSS	Fetal Lung	lung
20	chr19:36912000-36913000	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
21	chr19:36912000-36913000	Flanking Active TSS	Placenta	Placenta
22	chr19:36912000-36913000	Active TSS	Placenta Amnion	Placenta Amnion
23	chr19:36912000-36913000	Active TSS	Rectal Smooth Muscle	rectum
24	chr19:36912000-36913000	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
25	chr19:36912000-36913000	ZNF genes & repeats	HSMM	muscle
26	chr19:36912000-36913200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
27	chr19:36912000-36913200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr19:36912000-36913200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr19:36912000-36913200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr19:36912000-36913200	Active TSS	Brain Anterior Caudate	brain
31	chr19:36912000-36913200	Active TSS	Brain Cingulate Gyrus	brain
32	chr19:36912000-36913200	Bivalent/Poised TSS	Fetal Brain Female	brain
33	chr19:36912000-36913200	Active TSS	Pancreatic Islets	Pancreatic Islet
34	chr19:36912000-36913200	ZNF genes & repeats	Gastric	stomach
35	chr19:36912000-36913200	ZNF genes & repeats	Lung	lung
36	chr19:36912000-36913200	ZNF genes & repeats	Spleen	Spleen
37	chr19:36912000-36913200	Active TSS	Osteobl	bone
38	chr19:36912000-36913400	Active TSS	Brain Angular Gyrus	brain
39	chr19:36912000-36913600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr19:36912200-36912600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr19:36912200-36912600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
42	chr19:36912200-36912600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr19:36912200-36912800	Flanking Active TSS	Primary hematopoietic stem cells	blood
44	chr19:36912200-36912800	Active TSS	Muscle Satellite Cultured Cells	--
45	chr19:36912200-36912800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr19:36912200-36912800	Active TSS	Aorta	Aorta
47	chr19:36912200-36912800	Active TSS	Left Ventricle	heart
48	chr19:36912200-36912800	Active TSS	Ovary	ovary
49	chr19:36912200-36912800	Active TSS	Stomach Smooth Muscle	stomach
50	chr19:36912200-36912800	Active TSS	HSMMtube	muscle

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