Variant report

Variant	rs7258517
Chromosome Location	chr19:44535999-44536000
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:44528545..44530793-chr19:44535583..44538948,4	K562	blood:
2	chr19:44535327..44537229-chr19:44540572..44542738,2	K562	blood:
3	chr19:44534267..44536830-chr19:44544823..44547468,2	K562	blood:
4	chr19:44535729..44539292-chr19:44539752..44542558,4	K562	blood:

Variant related genes	Relation type
ENSG00000267022	Chromatin interaction
ENSG00000159885	Chromatin interaction
ENSG00000267144	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10418363	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11083732	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11083733	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11881151	0.84[ASN][1000 genomes]
rs12232810	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1996408	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2191566	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2270196	0.82[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2356549	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs367209	0.82[CEU][hapmap];0.85[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs367499	0.92[ASN][1000 genomes]
rs369106	0.82[CEU][hapmap];0.85[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs377503	0.83[ASN][1000 genomes]
rs3810406	0.92[ASW][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.88[LWK][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs384544	0.92[ASN][1000 genomes]
rs390369	0.82[CEU][hapmap];0.85[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4433920	0.85[ASN][1000 genomes]
rs4482396	0.86[ASN][1000 genomes]
rs4803667	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4803669	0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs4803675	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs55703004	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56171514	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56317065	0.85[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs59963278	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62115482	0.84[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs62115484	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs62115489	0.83[ASN][1000 genomes]
rs62119173	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62119176	0.94[ASN][1000 genomes]
rs6509133	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6509138	1.00[ASW][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.94[LWK][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.85[ASN][1000 genomes]
rs7245749	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7252394	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7253205	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7254261	0.92[ASW][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.88[LWK][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.87[YRI][hapmap];0.83[ASN][1000 genomes]
rs7254907	0.87[ASN][1000 genomes]
rs7255145	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7255315	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7255512	1.00[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.85[ASN][1000 genomes]
rs7256908	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7260075	0.85[ASN][1000 genomes]
rs73037629	0.88[ASN][1000 genomes]
rs8104605	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs8105571	1.00[ASW][hapmap];0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.87[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469650	chr19:44405994-44555426	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv833840	chr19:44520620-44715760	Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7258517	OPA3	cis	cerebellum	SCAN
rs7258517	FOXA3	cis	cerebellum	SCAN
rs7258517	HIF3A	cis	parietal	SCAN
rs7258517	RRAS	cis	cerebellum	SCAN
rs7258517	OPA3	cis	parietal	SCAN
rs7258517	PTGIR	cis	cerebellum	SCAN
rs7258517	CCDC114	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44530400-44536200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:44530800-44537000	ZNF genes & repeats	Fetal Kidney	kidney
3	chr19:44530800-44537000	ZNF genes & repeats	Fetal Lung	lung
4	chr19:44530800-44537200	ZNF genes & repeats	Ovary	ovary
5	chr19:44530800-44539200	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
6	chr19:44530800-44539600	ZNF genes & repeats	Fetal Brain Female	brain
7	chr19:44530800-44542600	ZNF genes & repeats	Liver	Liver
8	chr19:44531000-44536400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr19:44531000-44537000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr19:44531000-44537000	ZNF genes & repeats	Primary B cells from cord blood	blood
11	chr19:44531000-44537000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
12	chr19:44531000-44537000	ZNF genes & repeats	Aorta	Aorta
13	chr19:44531000-44537000	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
14	chr19:44531000-44537000	ZNF genes & repeats	Stomach Smooth Muscle	stomach
15	chr19:44531000-44537000	ZNF genes & repeats	Thymus	Thymus
16	chr19:44531000-44537200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr19:44531000-44537200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr19:44531000-44537200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
19	chr19:44531000-44538000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
20	chr19:44531000-44538200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
21	chr19:44531000-44538200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr19:44531000-44538400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr19:44531000-44539400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
24	chr19:44531000-44540000	ZNF genes & repeats	Adipose Nuclei	Adipose
25	chr19:44531200-44536600	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
26	chr19:44531200-44536800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr19:44531200-44537000	ZNF genes & repeats	Colon Smooth Muscle	Colon
28	chr19:44531200-44537200	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
29	chr19:44531200-44537400	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
30	chr19:44531200-44537600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
31	chr19:44531400-44536000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr19:44531400-44536000	Weak transcription	Hela-S3	cervix
33	chr19:44531400-44537200	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
34	chr19:44531600-44537000	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
35	chr19:44531600-44537000	Strong transcription	Placenta Amnion	Placenta Amnion
36	chr19:44531800-44537000	ZNF genes & repeats	Primary T cells from cord blood	blood
37	chr19:44531800-44537000	ZNF genes & repeats	Psoas Muscle	Psoas
38	chr19:44531800-44537000	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
39	chr19:44531800-44537200	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
40	chr19:44531800-44537200	ZNF genes & repeats	GM12878-XiMat	blood
41	chr19:44532000-44536800	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--
42	chr19:44532000-44537400	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
43	chr19:44532200-44536000	Strong transcription	NHDF-Ad	bronchial
44	chr19:44532200-44536600	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
45	chr19:44532200-44536800	ZNF genes & repeats	Primary T helper naive cells from peripheral blood	blood
46	chr19:44532200-44537000	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
47	chr19:44532200-44537000	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
48	chr19:44532200-44537000	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
49	chr19:44532200-44537000	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
50	chr19:44532200-44537000	ZNF genes & repeats	Brain Cingulate Gyrus	brain

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