Variant report

Variant	rs7255512
Chromosome Location	chr19:44574700-44574701
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:44554851..44557017-chr19:44574695..44576778,3	MCF-7	breast:
2	chr19:44554677..44558669-chr19:44574332..44578828,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000178386	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs10418363	0.81[ASN][1000 genomes]
rs11083732	0.81[ASN][1000 genomes]
rs11083733	0.81[ASN][1000 genomes]
rs12232810	0.95[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs1996408	1.00[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.84[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];0.80[ASN][1000 genomes]
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[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs390369	0.85[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap]
rs4433920	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4482396	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4803667	1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs4803669	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4803673	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4803675	0.92[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55771992	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55812285	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56149185	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56182773	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56317065	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56320525	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62115482	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62115484	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62115489	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62115511	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62115513	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62119173	0.81[ASN][1000 genomes]
rs62119176	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6509133	0.81[ASN][1000 genomes]
rs6509138	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];1.00[ASN][1000 genomes]
rs7245749	0.95[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs7246834	0.85[AMR][1000 genomes]
rs7254261	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]
rs7254907	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7255145	0.83[ASN][1000 genomes]
rs7255315	0.95[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs7255701	0.87[EUR][1000 genomes]
rs7256908	0.95[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs7258517	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]
rs7260075	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73037629	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8104437	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8104605	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8104802	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8105315	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8105571	0.95[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs8105574	0.87[EUR][1000 genomes];0.82[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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs7255512	HIF3A	cis	parietal	SCAN
rs7255512	CCDC114	cis	cerebellum	SCAN
rs7255512	OPA3	cis	parietal	SCAN
rs7255512	FOXA3	cis	cerebellum	SCAN
rs7255512	FUZ	cis	cerebellum	SCAN
rs7255512	PTGIR	cis	cerebellum	SCAN
rs7255512	OPA3	cis	cerebellum	SCAN
rs7255512	APOC4	cis	parietal	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44557000-44575600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:44558200-44575600	ZNF genes & repeats	Liver	Liver
3	chr19:44568000-44575400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr19:44570600-44575400	Weak transcription	HepG2	liver
5	chr19:44571200-44575600	Weak transcription	Right Ventricle	heart
6	chr19:44571200-44575800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr19:44571400-44575000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr19:44571400-44575400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr19:44571400-44575400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr19:44571400-44575600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr19:44571400-44575600	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr19:44571400-44575600	Weak transcription	Fetal Thymus	thymus
13	chr19:44571600-44575400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr19:44571800-44575400	Weak transcription	Brain Cingulate Gyrus	brain
15	chr19:44571800-44575400	Weak transcription	Brain Substantia Nigra	brain
16	chr19:44571800-44575600	Weak transcription	Thymus	Thymus
17	chr19:44571800-44575800	Weak transcription	HUVEC	blood vessel
18	chr19:44572000-44575400	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr19:44572000-44575600	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr19:44572000-44575600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr19:44572000-44575600	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr19:44572000-44575600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr19:44572000-44575600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr19:44572000-44575600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr19:44572000-44575600	Weak transcription	Colonic Mucosa	Colon
26	chr19:44572000-44575600	Weak transcription	Fetal Brain Male	brain
27	chr19:44572000-44575600	Weak transcription	Fetal Heart	heart
28	chr19:44572000-44575600	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr19:44572000-44575600	Weak transcription	NH-A	brain
30	chr19:44572000-44575600	Weak transcription	Osteobl	bone
31	chr19:44572000-44575800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr19:44572000-44575800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr19:44572000-44575800	Weak transcription	Fetal Kidney	kidney
34	chr19:44572000-44575800	Weak transcription	NHDF-Ad	bronchial
35	chr19:44572000-44575800	Weak transcription	NHLF	lung
36	chr19:44572200-44575200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr19:44572200-44575400	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr19:44572200-44575400	Weak transcription	Brain Hippocampus Middle	brain
39	chr19:44572200-44575600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr19:44572200-44575600	Weak transcription	Brain Anterior Caudate	brain
41	chr19:44572200-44575600	Weak transcription	Colon Smooth Muscle	Colon
42	chr19:44572200-44575600	Weak transcription	Left Ventricle	heart
43	chr19:44572200-44575800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr19:44572400-44575800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr19:44572600-44575200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr19:44572600-44575200	Weak transcription	Psoas Muscle	Psoas
47	chr19:44572600-44575400	Weak transcription	Brain Angular Gyrus	brain
48	chr19:44572600-44575600	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr19:44572600-44575800	Weak transcription	Ovary	ovary
50	chr19:44572800-44575400	Weak transcription	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links