Variant report

Variant	rs12983292
Chromosome Location	chr19:19787767-19787768
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:19787138..19789132-chr19:19790779..19792628,2	K562	blood:

Variant related genes	Relation type
ENSG00000181896	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10402516	0.83[ASN][1000 genomes]
rs10405234	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10421328	0.89[CEU][hapmap];0.86[TSI][hapmap]
rs10423311	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11667828	1.00[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11667844	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11670710	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];0.99[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12974308	0.99[ASN][1000 genomes]
rs12976582	0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12980482	0.96[ASN][1000 genomes]
rs12982049	0.99[ASN][1000 genomes]
rs12982500	0.99[ASN][1000 genomes]
rs1433079	0.83[ASN][1000 genomes]
rs16996227	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2288865	0.89[CEU][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2288867	0.94[CEU][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28635562	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34558847	0.97[ASN][1000 genomes]
rs35035906	0.83[ASN][1000 genomes]
rs35445661	0.89[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs35449009	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs35792080	0.97[ASN][1000 genomes]
rs35801717	0.99[ASN][1000 genomes]
rs3752152	0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs3794996	1.00[JPT][hapmap]
rs4808209	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4808976	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4808979	0.86[ASN][1000 genomes]
rs4808981	0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs55831814	0.81[EUR][1000 genomes]
rs7247142	0.90[ASN][1000 genomes]
rs7249670	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7251924	0.94[ASN][1000 genomes]
rs74181147	0.99[ASN][1000 genomes]
rs74181148	0.99[ASN][1000 genomes]
rs74181149	0.99[ASN][1000 genomes]
rs74181150	0.99[ASN][1000 genomes]
rs74181151	0.99[ASN][1000 genomes]
rs8107058	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs919778	0.89[CEU][hapmap];0.81[TSI][hapmap]

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	esv1828240	chr19:19591146-19900900	Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1063273	chr19:19591146-20061367	ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	esv3330851	chr19:19755507-19852881	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12983292	MED26	cis	parietal	SCAN
rs12983292	ZNF14	cis	parietal	SCAN
rs12983292	ZNF738	cis	cerebellum	SCAN
rs12983292	ZNF14	cis	cerebellum	SCAN
rs12983292	C19orf60	cis	parietal	SCAN
rs12983292	OR10H4	cis	parietal	SCAN
rs12983292	UNC13A	cis	cerebellum	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19780200-19788200	Weak transcription	Aorta	Aorta
2	chr19:19780200-19789800	Weak transcription	Fetal Brain Male	brain
3	chr19:19780200-19790000	Weak transcription	Fetal Heart	heart
4	chr19:19780600-19788800	Weak transcription	Fetal Kidney	kidney
5	chr19:19780600-19788800	Weak transcription	HSMMtube	muscle
6	chr19:19780600-19790000	Weak transcription	Brain Cingulate Gyrus	brain
7	chr19:19780600-19795000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr19:19780800-19787800	Weak transcription	NHDF-Ad	bronchial
9	chr19:19780800-19788200	Weak transcription	HUVEC	blood vessel
10	chr19:19780800-19789800	Weak transcription	Psoas Muscle	Psoas
11	chr19:19780800-19790000	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr19:19780800-19795000	ZNF genes & repeats	Fetal Thymus	thymus
13	chr19:19780800-19795000	ZNF genes & repeats	Thymus	Thymus
14	chr19:19781000-19787800	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr19:19781000-19788000	Weak transcription	Brain Anterior Caudate	brain
16	chr19:19781000-19788200	Weak transcription	Brain Angular Gyrus	brain
17	chr19:19781000-19788200	Weak transcription	Brain Hippocampus Middle	brain
18	chr19:19781000-19788200	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr19:19781000-19788400	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr19:19781000-19788400	Weak transcription	Fetal Lung	lung
21	chr19:19781000-19788400	Weak transcription	Stomach Smooth Muscle	stomach
22	chr19:19781000-19789600	Weak transcription	Fetal Brain Female	brain
23	chr19:19781000-19789800	Weak transcription	Brain Substantia Nigra	brain
24	chr19:19781000-19792600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr19:19781200-19787800	Weak transcription	Hela-S3	cervix
26	chr19:19781200-19787800	Weak transcription	Osteobl	bone
27	chr19:19781200-19788000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr19:19781200-19788200	Weak transcription	Rectal Smooth Muscle	rectum
29	chr19:19781200-19788200	Weak transcription	Stomach Mucosa	stomach
30	chr19:19781200-19789800	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr19:19781200-19790000	Weak transcription	Colon Smooth Muscle	Colon
32	chr19:19781200-19795800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
33	chr19:19781400-19788000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr19:19781400-19788000	Weak transcription	Left Ventricle	heart
35	chr19:19781400-19788200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr19:19781400-19788200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr19:19781400-19788200	Weak transcription	Pancreas	Pancrea
38	chr19:19781400-19790000	Weak transcription	Right Ventricle	heart
39	chr19:19781400-19792800	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
40	chr19:19781400-19793000	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
41	chr19:19781400-19793400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr19:19781600-19788000	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr19:19781600-19788200	Weak transcription	Gastric	stomach
44	chr19:19781600-19789200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr19:19781600-19795000	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
46	chr19:19781800-19794400	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
47	chr19:19782000-19788200	Weak transcription	Placenta	Placenta
48	chr19:19782000-19795000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr19:19782000-19795600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
50	chr19:19782000-19798200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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