Variant report

Variant	rs689544
Chromosome Location	chr5:90328537-90328538
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	chr5:90325968..90328766-chr5:90677974..90679493,2	K562	blood:

Variant related genes	Relation type
ENSG00000113369	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10038122	0.88[CEU][hapmap];0.87[LWK][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs10055587	0.81[EUR][1000 genomes]
rs10058319	0.81[EUR][1000 genomes]
rs10942624	0.88[ASN][1000 genomes]
rs12109264	0.86[YRI][hapmap]
rs12186662	0.84[ASN][1000 genomes]
rs13179479	0.99[ASN][1000 genomes]
rs13180409	0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs16869403	1.00[YRI][hapmap]
rs1819073	0.95[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs1819074	0.95[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs1828177	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1828178	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1848481	0.81[EUR][1000 genomes]
rs1848483	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs1848484	0.81[EUR][1000 genomes]
rs1848485	0.88[CEU][hapmap];0.83[LWK][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs1848486	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs1848487	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs1852734	0.91[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs1858070	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]
rs1976565	0.88[CEU][hapmap];0.91[LWK][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs2048217	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2367185	0.87[CEU][hapmap];0.80[TSI][hapmap]
rs2367186	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2367274	0.88[ASN][1000 genomes]
rs2463775	0.91[ASN][1000 genomes]
rs2662278	0.88[ASN][1000 genomes]
rs2662279	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2662280	0.86[JPT][hapmap]
rs2662281	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2662282	0.99[ASN][1000 genomes]
rs2662283	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2662284	0.95[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs2697543	0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs2697544	0.88[ASN][1000 genomes]
rs2697546	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2697547	0.83[EUR][1000 genomes]
rs28875340	0.94[ASN][1000 genomes]
rs2973444	0.81[YRI][hapmap]
rs2973448	0.82[YRI][hapmap]
rs4254936	0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs4391205	0.81[EUR][1000 genomes]
rs4454077	0.88[ASN][1000 genomes]
rs4916838	0.81[EUR][1000 genomes]
rs4916839	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs4916840	0.81[EUR][1000 genomes]
rs6452928	0.88[CEU][hapmap];0.87[LWK][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs6452930	0.95[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs6452934	0.95[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs6865615	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs7706034	0.95[CHB][hapmap];0.91[CHD][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs7719311	0.95[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs7723511	0.95[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs7733024	0.82[LWK][hapmap]
rs7733230	0.95[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs937920	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs998788	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][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	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
rs689544	GPR98	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:90323600-90330400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:90323600-90332800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr5:90324200-90329000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr5:90324200-90330400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:90324200-90332800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr5:90324200-90332800	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr5:90324600-90335200	Weak transcription	Small Intestine	intestine
8	chr5:90324600-90350400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr5:90324800-90329200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr5:90325000-90328600	Weak transcription	Colon Smooth Muscle	Colon
11	chr5:90326400-90329400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr5:90327200-90328800	Weak transcription	Liver	Liver
13	chr5:90327400-90328600	Weak transcription	A549	lung
14	chr5:90327400-90329200	Weak transcription	Fetal Intestine Large	intestine
15	chr5:90327400-90329200	Weak transcription	Fetal Intestine Small	intestine

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