Variant report

Variant	rs73043902
Chromosome Location	chr19:36908677-36908678
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	E2F6	chr19:36908594-36910011	H1-hESC	embryonic stem cell:	n/a	chr19:36909599-36909609 chr19:36909597-36909606 chr19:36909718-36909733
2	MAX	chr19:36908512-36909936	K562	blood:	n/a	n/a
3	MAX	chr19:36908607-36909821	GM12878	blood:	n/a	n/a
4	MAZ	chr19:36908601-36910028	IMR90	lung:	n/a	n/a
5	MAX	chr19:36908588-36910199	A549	lung:	n/a	n/a
6	RCOR1	chr19:36908014-36910259	IMR90	lung:	n/a	n/a
7	BHLHE40	chr19:36908676-36908833	K562	blood:	n/a	n/a
8	E2F6	chr19:36908631-36909172	K562	blood:	n/a	n/a
9	TCF12	chr19:36908645-36909802	A549	lung:	n/a	n/a
10	BHLHE40	chr19:36908569-36908892	GM12878	blood:	n/a	n/a
11	MAX	chr19:36908607-36909957	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000267142	TF binding region

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12461529	0.88[ASN][1000 genomes]
rs12462725	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17206379	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2271842	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2385802	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2857	0.88[ASN][1000 genomes]
rs2945955	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2945956	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2945989	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2967508	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2967511	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2967516	0.82[ASN][1000 genomes]
rs2967519	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3098393	0.88[ASN][1000 genomes]
rs3111555	0.81[ASN][1000 genomes]
rs3111556	0.88[ASN][1000 genomes]
rs3810326	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56378871	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61706074	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62112567	0.88[ASN][1000 genomes]
rs62112568	0.88[ASN][1000 genomes]
rs62112569	0.88[ASN][1000 genomes]
rs62112624	0.88[ASN][1000 genomes]
rs62112631	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62112632	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62113869	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7253122	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73043845	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8104241	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs73043902	LINC00665	cis	Muscle Skeletal	GTEx
rs73043902	LINC00665	cis	Nerve Tibial	GTEx
rs73043902	LINC00665	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36882200-36908800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:36905600-36908800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr19:36907000-36909400	Transcr. at gene 5' and 3'	Dnd41	blood
4	chr19:36907400-36908800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr19:36907800-36910000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr19:36908000-36908800	ZNF genes & repeats	GM12878-XiMat	blood
7	chr19:36908000-36909000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr19:36908000-36909000	ZNF genes & repeats	HMEC	breast
9	chr19:36908000-36909200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr19:36908000-36909200	Flanking Active TSS	Duodenum Mucosa	Duodenum
11	chr19:36908000-36909800	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr19:36908000-36909800	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr19:36908000-36910000	Active TSS	K562	blood
14	chr19:36908200-36908800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr19:36908200-36908800	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr19:36908200-36908800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
17	chr19:36908200-36908800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr19:36908200-36908800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr19:36908200-36908800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr19:36908200-36908800	Flanking Active TSS	Brain Angular Gyrus	brain
21	chr19:36908200-36908800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
22	chr19:36908200-36908800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
23	chr19:36908200-36908800	Flanking Active TSS	Brain Substantia Nigra	brain
24	chr19:36908200-36908800	Flanking Active TSS	Fetal Lung	lung
25	chr19:36908200-36908800	Enhancers	Spleen	Spleen
26	chr19:36908200-36908800	ZNF genes & repeats	HSMM	muscle
27	chr19:36908200-36909000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr19:36908200-36909000	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
29	chr19:36908200-36909000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
30	chr19:36908200-36909000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
31	chr19:36908200-36909000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
32	chr19:36908200-36909000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr19:36908200-36909000	Flanking Active TSS	Brain Germinal Matrix	brain
34	chr19:36908200-36909000	Flanking Active TSS	Brain Hippocampus Middle	brain
35	chr19:36908200-36909000	Flanking Active TSS	Colon Smooth Muscle	Colon
36	chr19:36908200-36909000	Flanking Active TSS	Fetal Brain Male	brain
37	chr19:36908200-36909000	Flanking Active TSS	Fetal Heart	heart
38	chr19:36908200-36909000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
39	chr19:36908200-36909200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
40	chr19:36908200-36909200	Flanking Active TSS	Stomach Smooth Muscle	stomach
41	chr19:36908200-36909200	ZNF genes & repeats	A549	lung
42	chr19:36908200-36909400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr19:36908200-36909800	Active TSS	HUES64 Cell Line	embryonic stem cell
44	chr19:36908200-36910000	Active TSS	H1 Cell Line	embryonic stem cell
45	chr19:36908200-36910000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr19:36908200-36910000	Active TSS	HUES6 Cell Line	embryonic stem cell
47	chr19:36908200-36910000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr19:36908200-36910000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr19:36908200-36910000	Active TSS	Pancreatic Islets	Pancreatic Islet
50	chr19:36908200-36910000	Active TSS	Ovary	ovary

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