Variant report

Variant	rs2967496
Chromosome Location	chr19:36819170-36819171
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	POLR2A	chr19:36818873-36819306	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr19:36817485-36819387	H1-hESC	embryonic stem cell:	n/a	n/a
3	ZNF263	chr19:36818899-36819255	HEK293-T-REx	kidney:	n/a	n/a

Variant related genes	Relation type
ENSG00000222730	TF binding region

Extended variants
information (count: 65 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10404574	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10418510	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10420610	0.80[EUR][1000 genomes]
rs10439091	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12459465	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12971694	0.82[ASN][1000 genomes]
rs12976881	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12986029	0.80[EUR][1000 genomes]
rs2385799	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2385800	0.80[AFR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2385803	0.80[AFR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2385805	0.80[AFR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2918349	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2945945	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2945949	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2945950	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2945951	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2945957	0.80[AFR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2945961	0.82[AFR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2945963	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2945971	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2945972	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2945993	0.80[AFR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2945995	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2967484	0.87[AFR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2967493	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2967501	0.92[AFR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2967506	0.86[ASN][1000 genomes]
rs2967509	0.82[ASN][1000 genomes]
rs2967510	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2967512	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2967515	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2967517	0.82[AFR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2967518	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2967521	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2972632	0.80[ASN][1000 genomes]
rs2972633	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4806321	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5021030	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62112565	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6417185	0.80[AFR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6510541	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7251979	0.80[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7255260	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7255403	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8106095	0.86[ASN][1000 genomes]
rs8109320	0.80[AFR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8109333	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8112312	0.80[AFR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8182628	0.80[AFR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520020	chr19:36721368-36822594	Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv1063208	chr19:36743461-36847486	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1056901	chr19:36749658-36847486	Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1061054	chr19:36751703-36847486	Strong transcription Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1055260	chr19:36752221-36847486	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1056850	chr19:36752663-36847486	Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv1064983	chr19:36752663-36847625	Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv1057579	chr19:36752663-36847822	Strong transcription Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
9	esv1825146	chr19:36800927-36846993	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
10	esv1837043	chr19:36800927-36846993	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv2474	chr19:36804469-36865415	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	esv2763143	chr19:36805705-36847498	Strong transcription Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv1059568	chr19:36806475-36847864	Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
14	esv1823621	chr19:36807288-36845863	Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent/Poised TSS	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
15	nsv1064343	chr19:36807288-36853102	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2967496	LINC00665	cis	Nerve Tibial	GTEx
rs2967496	LOC284412	N/A	lymphoblastoid	RTeQTL
rs2967496	LINC00665	cis	Muscle Skeletal	GTEx

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36800800-36822000	Weak transcription	Psoas Muscle	Psoas
2	chr19:36804000-36820600	Strong transcription	HUES48 Cell Line	embryonic stem cell
3	chr19:36804800-36820800	Weak transcription	Brain Angular Gyrus	brain
4	chr19:36805400-36822000	Weak transcription	HSMMtube	muscle
5	chr19:36805800-36821000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr19:36806400-36820600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
7	chr19:36806600-36821000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr19:36806600-36822000	Weak transcription	Rectal Smooth Muscle	rectum
9	chr19:36806800-36820000	Strong transcription	H1 Cell Line	embryonic stem cell
10	chr19:36808600-36820000	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr19:36810000-36820200	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr19:36810400-36820800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr19:36810600-36820600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr19:36812800-36821600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
15	chr19:36813200-36821000	Strong transcription	Fetal Muscle Trunk	muscle
16	chr19:36813200-36821800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr19:36813400-36819200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr19:36813400-36821400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr19:36813400-36821800	Weak transcription	Brain Substantia Nigra	brain
20	chr19:36813600-36821800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr19:36814000-36819600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr19:36814600-36821000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr19:36814800-36820600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr19:36814800-36820800	Strong transcription	Brain Germinal Matrix	brain
25	chr19:36814800-36821400	Strong transcription	Fetal Muscle Leg	muscle
26	chr19:36815200-36821000	Strong transcription	Fetal Brain Female	brain
27	chr19:36815200-36822000	Weak transcription	NHLF	lung
28	chr19:36815400-36821200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr19:36815400-36822000	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr19:36815800-36820200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr19:36815800-36821000	Strong transcription	Fetal Stomach	stomach
32	chr19:36815800-36821200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr19:36815800-36821400	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr19:36815800-36821400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr19:36815800-36821800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr19:36816200-36819400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr19:36816200-36821000	Weak transcription	HSMM	muscle
38	chr19:36816200-36821400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
39	chr19:36816400-36819400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr19:36816400-36819400	ZNF genes & repeats	Aorta	Aorta
41	chr19:36816400-36819600	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr19:36816400-36820200	Strong transcription	Left Ventricle	heart
43	chr19:36816400-36820400	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr19:36816400-36820400	Strong transcription	Fetal Intestine Large	intestine
45	chr19:36816400-36820600	Strong transcription	H9 Cell Line	embryonic stem cell
46	chr19:36816400-36820600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr19:36816400-36821000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr19:36816400-36821000	Strong transcription	Primary B cells from peripheral blood	blood
49	chr19:36816400-36821200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr19:36816400-36821200	Strong transcription	Brain Inferior Temporal Lobe	brain

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