Variant report

Variant	rs2247870
Chromosome Location	chr5:90151589-90151590
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:90150790..90152921-chr5:90154624..90158085,3	K562	blood:
2	chr5:90146306..90149323-chr5:90149920..90152363,3	K562	blood:
3	chr5:90145396..90148045-chr5:90150505..90152535,3	K562	blood:

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12519770	0.86[CHB][hapmap];0.84[GIH][hapmap]
rs13159353	0.85[EUR][1000 genomes]
rs13188479	0.85[CHB][hapmap]
rs2244356	0.84[ASN][1000 genomes]
rs2247415	0.86[EUR][1000 genomes]
rs2247419	0.90[EUR][1000 genomes]
rs2247546	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2438338	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs2438342	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs2438343	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs2438344	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs2438345	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs2438352	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs2438355	0.86[CHB][hapmap]
rs2438362	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs2443079	0.81[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2443085	0.86[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2443089	0.89[EUR][1000 genomes]
rs2443091	0.95[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2460167	0.86[CHB][hapmap]
rs3098356	0.85[CEU][hapmap];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529544	chr5:89523963-90412409	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv882367	chr5:89956991-90209824	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
3	nsv1015449	chr5:89968626-90219398	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv517049	chr5:90003131-90262475	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2247870	GPR98	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:90112000-90160600	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr5:90112000-90175800	Weak transcription	Fetal Brain Female	brain
3	chr5:90142400-90156200	Weak transcription	Fetal Brain Male	brain
4	chr5:90142600-90162400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr5:90145200-90153400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
6	chr5:90145600-90153200	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr5:90146800-90152600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr5:90148200-90171400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr5:90148400-90155200	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr5:90148400-90164800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr5:90148600-90152000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr5:90149400-90151800	Strong transcription	H1 Cell Line	embryonic stem cell
13	chr5:90149400-90152000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr5:90149600-90151600	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr5:90149600-90151800	Enhancers	Primary hematopoietic stem cells	blood
16	chr5:90150400-90158200	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr5:90150400-90159800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr5:90150600-90152200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr5:90151000-90151600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr5:90151200-90151600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr5:90151200-90151600	Strong transcription	K562	blood
22	chr5:90151200-90151800	Strong transcription	H9 Cell Line	embryonic stem cell
23	chr5:90151200-90151800	Enhancers	HMEC	breast
24	chr5:90151200-90152000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr5:90151200-90152000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr5:90151200-90152000	Enhancers	NHEK	skin
27	chr5:90151200-90152200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr5:90151400-90152200	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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