Variant report

Variant	rs7254261
Chromosome Location	chr19:44565427-44565428
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	chr19:44563861..44566757-chr19:44575129..44577196,2	MCF-7	breast:
2	chr19:44564682..44566396-chr19:44596873..44599665,3	K562	blood:

Variant related genes	Relation type
ENSG00000267680	Chromatin interaction
ENSG00000186026	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 9 )

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

rs_ID	r²[population]
rs12232810	0.95[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap]
rs1996408	1.00[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.83[ASN][1000 genomes]
rs2191566	0.95[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap]
rs2270196	0.85[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap]
rs2356549	0.95[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap]
rs367209	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs369106	0.85[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap]
rs3810406	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs390369	0.85[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap]
rs4433920	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4482396	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4803667	1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap];0.83[ASN][1000 genomes]
rs4803669	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4803673	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4803675	0.92[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55771992	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs55812285	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56149185	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56182773	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56317065	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56320525	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62115482	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62115484	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62115489	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62115511	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62115513	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62119176	0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6509138	0.92[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];0.98[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7245749	0.95[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap]
rs7246834	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7254907	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7255145	0.82[ASN][1000 genomes]
rs7255315	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs7255512	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7255701	0.88[EUR][1000 genomes]
rs7256908	0.95[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap]
rs7258517	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]
rs7260075	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73037629	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8104437	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8104605	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8104802	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8105315	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8105571	0.92[ASW][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap]
rs8105574	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs7254261	FOXA3	cis	cerebellum	SCAN
rs7254261	OPA3	cis	parietal	SCAN
rs7254261	APOC4	cis	parietal	SCAN
rs7254261	CCDC114	cis	cerebellum	SCAN
rs7254261	ZNF155	cis	multi-tissue	Pritchard
rs7254261	HIF3A	cis	parietal	SCAN
rs7254261	OPA3	cis	cerebellum	SCAN
rs7254261	FUZ	cis	cerebellum	SCAN
rs7254261	PTGIR	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44557000-44566800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:44557000-44567400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr19:44557000-44567400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr19:44557000-44567600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr19:44557000-44568800	Weak transcription	HMEC	breast
6	chr19:44557000-44570200	Weak transcription	HUVEC	blood vessel
7	chr19:44557000-44570200	Weak transcription	NHDF-Ad	bronchial
8	chr19:44557000-44575600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr19:44557200-44565600	Weak transcription	NHLF	lung
10	chr19:44557400-44570000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr19:44557400-44570200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr19:44558200-44571800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr19:44558200-44573200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr19:44558200-44575600	ZNF genes & repeats	Liver	Liver
15	chr19:44558800-44567800	Strong transcription	Stomach Smooth Muscle	stomach
16	chr19:44558800-44572800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
17	chr19:44559200-44569000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr19:44559200-44569000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr19:44559200-44569400	Strong transcription	Fetal Stomach	stomach
20	chr19:44559400-44565800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr19:44559400-44569400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr19:44559400-44570000	Weak transcription	Stomach Mucosa	stomach
23	chr19:44559600-44565800	Strong transcription	Colonic Mucosa	Colon
24	chr19:44559800-44568600	Strong transcription	HSMMtube	muscle
25	chr19:44560000-44568800	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr19:44560200-44567200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr19:44560400-44566400	Weak transcription	Fetal Thymus	thymus
28	chr19:44560400-44566800	Weak transcription	NHEK	skin
29	chr19:44560800-44569400	Strong transcription	Fetal Intestine Large	intestine
30	chr19:44560800-44570000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr19:44561000-44568800	Strong transcription	Fetal Brain Female	brain
32	chr19:44561000-44569200	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr19:44561200-44569600	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr19:44561400-44568400	Strong transcription	Brain Angular Gyrus	brain
35	chr19:44561400-44568800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr19:44561400-44569000	Strong transcription	Fetal Muscle Trunk	muscle
37	chr19:44561400-44570000	Strong transcription	Brain Hippocampus Middle	brain
38	chr19:44561600-44566000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr19:44561600-44567400	Strong transcription	Sigmoid Colon	Sigmoid Colon
40	chr19:44561600-44568800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr19:44561600-44569000	Strong transcription	Brain Inferior Temporal Lobe	brain
42	chr19:44561600-44569600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr19:44561800-44565600	Strong transcription	Left Ventricle	heart
44	chr19:44561800-44566000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
45	chr19:44561800-44566000	ZNF genes & repeats	Esophagus	oesophagus
46	chr19:44561800-44566000	ZNF genes & repeats	Pancreas	Pancrea
47	chr19:44561800-44566000	ZNF genes & repeats	Spleen	Spleen
48	chr19:44561800-44566000	Strong transcription	HepG2	liver
49	chr19:44561800-44566200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr19:44561800-44566200	ZNF genes & repeats	Lung	lung

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