Variant report

Variant	rs1858070
Chromosome Location	chr5:90337957-90337958
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:90331134..90333173-chr5:90336789..90338560,2	K562	blood:
2	chr5:90337875..90340059-chr5:90342694..90345036,3	K562	blood:
3	chr5:90331219..90333780-chr5:90335646..90338696,3	K562	blood:

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10038122	0.88[CEU][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs13180409	0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap]
rs16869403	0.89[YRI][hapmap]
rs1819073	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs1819074	0.95[CHB][hapmap];0.83[JPT][hapmap]
rs1828177	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs1828178	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs1848483	0.87[CEU][hapmap]
rs1848485	0.88[CEU][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs1848486	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs1848487	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs1852734	0.91[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap]
rs1976565	0.88[CEU][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs2048217	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2367185	0.87[CEU][hapmap]
rs2662279	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2662280	0.86[JPT][hapmap]
rs2662283	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2662284	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs2697543	0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap]
rs2697546	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4254936	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs4916839	0.87[CEU][hapmap]
rs6452928	0.88[CEU][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs6452930	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs6452934	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs6865615	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs689544	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap]
rs7706034	0.95[CHB][hapmap];0.91[CHD][hapmap];0.83[JPT][hapmap]
rs7719311	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs7723511	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs7733230	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs937920	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap]
rs998788	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]

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	nsv882369	chr5:90275825-90344149	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1024813	chr5:90321535-90870739	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
4	nsv537806	chr5:90321535-90870739	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1858070	GPR98	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:90324600-90350400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr5:90330800-90338000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr5:90334400-90338800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr5:90334600-90338800	Weak transcription	Adipose Nuclei	Adipose
5	chr5:90335000-90340600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr5:90335000-90340800	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr5:90335000-90344000	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr5:90335200-90344000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr5:90335400-90338600	Weak transcription	Colon Smooth Muscle	Colon
10	chr5:90335400-90338600	Weak transcription	Rectal Smooth Muscle	rectum
11	chr5:90335400-90340600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr5:90337600-90338800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr5:90337600-90339400	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr5:90337600-90339400	Enhancers	Fetal Intestine Large	intestine
15	chr5:90337600-90339600	Enhancers	Fetal Intestine Small	intestine
16	chr5:90337600-90339800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr5:90337600-90339800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr5:90337800-90339400	Enhancers	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links