Variant report

Variant	rs7258508
Chromosome Location	chr19:19475469-19475470
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:19469546..19472054-chr19:19474284..19475951,2	MCF-7	breast:
2	chr19:19475375..19475969-chr19:19600833..19601839,3	K562	blood:
3	chr19:19469138..19472356-chr19:19472972..19475692,3	K562	blood:

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10401193	0.81[EUR][1000 genomes]
rs10402661	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10403731	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10404728	0.81[EUR][1000 genomes]
rs10418051	0.85[AMR][1000 genomes]
rs10419672	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10421505	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11085259	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11085261	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11666553	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11669516	0.81[EUR][1000 genomes]
rs12459676	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12972397	0.82[EUR][1000 genomes]
rs12973258	0.85[EUR][1000 genomes]
rs12976025	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12977524	0.80[EUR][1000 genomes]
rs12982276	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12983137	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12985655	0.81[ASN][1000 genomes]
rs13964	0.82[ASN][1000 genomes]
rs1465695	0.81[EUR][1000 genomes]
rs15622	0.82[ASN][1000 genomes]
rs17288409	0.91[EUR][1000 genomes]
rs1859287	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2023883	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2074089	0.87[ASN][1000 genomes]
rs2074090	0.81[ASN][1000 genomes]
rs2074091	0.81[ASN][1000 genomes]
rs2074300	0.82[ASN][1000 genomes]
rs2074301	0.83[ASN][1000 genomes]
rs2099333	0.81[EUR][1000 genomes]
rs2163804	0.81[EUR][1000 genomes]
rs2163805	0.81[EUR][1000 genomes]
rs2285627	0.89[ASN][1000 genomes]
rs2285628	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2301668	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2301669	0.81[ASN][1000 genomes]
rs2301671	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28478453	0.81[EUR][1000 genomes]
rs2905423	0.82[ASN][1000 genomes]
rs2905424	0.90[ASN][1000 genomes]
rs2905425	0.90[ASN][1000 genomes]
rs2965191	0.81[ASN][1000 genomes]
rs2965193	0.81[ASN][1000 genomes]
rs2965198	0.90[ASN][1000 genomes]
rs2965199	0.90[ASN][1000 genomes]
rs4808194	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4808196	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4808199	0.86[EUR][1000 genomes]
rs4808939	0.83[ASN][1000 genomes]
rs4808950	0.83[EUR][1000 genomes]
rs4808960	0.81[EUR][1000 genomes]
rs60003758	0.82[EUR][1000 genomes]
rs60321073	0.90[EUR][1000 genomes]
rs6511032	0.81[ASN][1000 genomes]
rs67720221	0.86[ASN][1000 genomes]
rs7250368	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7250658	0.81[EUR][1000 genomes]
rs7259434	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs751858	0.81[EUR][1000 genomes]
rs754255	0.81[EUR][1000 genomes]
rs757000	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs757001	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs769267	0.81[ASN][1000 genomes]
rs8103197	0.81[ASN][1000 genomes]
rs8105094	0.81[ASN][1000 genomes]
rs8105984	0.81[ASN][1000 genomes]
rs8108647	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9304960	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs968525	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[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	nsv911303	chr19:19256870-19505087	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv911305	chr19:19303802-19663850	Genic enhancers Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv1056419	chr19:19421218-19510611	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7258508	KIAA0892	cis	multi-tissue	Pritchard

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19435600-19477600	Weak transcription	Fetal Heart	heart
2	chr19:19454400-19475600	Weak transcription	Fetal Kidney	kidney
3	chr19:19460800-19475600	Weak transcription	Psoas Muscle	Psoas
4	chr19:19465200-19483600	Weak transcription	NH-A	brain
5	chr19:19466600-19475600	Weak transcription	NHDF-Ad	bronchial
6	chr19:19466800-19475600	Weak transcription	HMEC	breast
7	chr19:19467200-19475600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr19:19467200-19477600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr19:19467400-19475600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr19:19467400-19475600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr19:19467400-19475600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr19:19467600-19475600	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr19:19467600-19475600	Weak transcription	HSMM	muscle
14	chr19:19468000-19475600	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr19:19468200-19477600	Weak transcription	Brain Substantia Nigra	brain
16	chr19:19468400-19476000	Weak transcription	Left Ventricle	heart
17	chr19:19468400-19477600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr19:19468400-19478000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr19:19468600-19477600	Weak transcription	Fetal Lung	lung
20	chr19:19468800-19475600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr19:19468800-19475600	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr19:19469200-19475600	Weak transcription	HSMMtube	muscle
23	chr19:19469200-19477600	Weak transcription	Brain Angular Gyrus	brain
24	chr19:19469400-19475800	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr19:19469400-19482000	Weak transcription	Esophagus	oesophagus
26	chr19:19469800-19475600	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr19:19469800-19476000	Weak transcription	Brain Anterior Caudate	brain
28	chr19:19469800-19477400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr19:19469800-19477400	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr19:19469800-19477600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr19:19469800-19488400	Weak transcription	Gastric	stomach
32	chr19:19470000-19477400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr19:19470000-19477600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr19:19470400-19477600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr19:19472200-19475600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr19:19472200-19475600	Weak transcription	Brain Cingulate Gyrus	brain
37	chr19:19472200-19477600	Weak transcription	Brain Hippocampus Middle	brain
38	chr19:19472400-19475600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr19:19472400-19475600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr19:19472400-19475600	Weak transcription	A549	lung
41	chr19:19472400-19475800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr19:19475200-19475600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr19:19475200-19475600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
44	chr19:19475200-19475600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
45	chr19:19475200-19475600	Enhancers	Stomach Mucosa	stomach
46	chr19:19475200-19476000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr19:19475200-19476000	Active TSS	Rectal Mucosa Donor 29	rectum
48	chr19:19475200-19476200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
49	chr19:19475200-19476200	Enhancers	Primary hematopoietic stem cells	blood
50	chr19:19475200-19476200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links