Variant report

Variant	rs250377
Chromosome Location	chr5:89839071-89839072
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:89838541..89840104-chr5:89852722..89854353,2	K562	blood:
2	chr5:89833046..89834867-chr5:89838183..89840243,2	K562	blood:
3	chr5:89829518..89831624-chr5:89838668..89840450,2	K562	blood:
4	chr5:89831265..89835125-chr5:89838183..89842442,4	K562	blood:
5	chr5:89710050..89711886-chr5:89838920..89841759,2	K562	blood:
6	chr5:89824636..89834797-chr5:89838005..89846568,18	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164199	Chromatin interaction
ENSG00000176018	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10069050	0.85[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.85[LWK][hapmap];0.87[MKK][hapmap];0.87[TSI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs149321	0.82[JPT][hapmap]
rs154568	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs154569	0.92[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs154570	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs154572	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs154573	0.87[EUR][1000 genomes]
rs1553545	1.00[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1673381	0.82[JPT][hapmap]
rs171790	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2366772	0.80[JPT][hapmap]
rs250366	0.82[JPT][hapmap]
rs257847	0.81[JPT][hapmap]
rs257850	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs257851	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2656957	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs27196	0.89[JPT][hapmap]
rs27197	0.82[JPT][hapmap]
rs27201	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs37238	1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.88[GIH][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs37239	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs37240	0.85[EUR][1000 genomes]
rs42467	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs43149	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4588621	0.81[JPT][hapmap]
rs491082	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5028525	0.82[JPT][hapmap]
rs511393	0.93[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.88[MKK][hapmap];0.87[TSI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs526806	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs556894	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59159252	0.96[ASN][1000 genomes]
rs594990	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs599432	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs625135	0.92[CEU][hapmap]
rs649449	0.82[JPT][hapmap]
rs656679	0.82[JPT][hapmap]
rs679568	0.96[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.85[AFR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6884154	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6892132	0.82[JPT][hapmap]
rs790081	0.83[CHD][hapmap]
rs810974	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021142	chr5:89102893-89897826	Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv537804	chr5:89102893-89897826	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv917025	chr5:89208994-89855436	Enhancers Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv432750	chr5:89410113-90137144	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv432751	chr5:89457044-90090444	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	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
7	nsv882365	chr5:89770768-89882618	Flanking Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases
8	nsv882366	chr5:89826726-89894564	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs250377	GPR98	cis	cerebellum	SCAN
rs250377	GPR98	cis	parietal	SCAN
rs250377	LYSMD3	cis	normal skin	skin_eQTL
rs250377	LYSMD3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:89826200-89842800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr5:89826800-89843200	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr5:89833800-89840400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:89838400-89840000	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr5:89838600-89839200	Enhancers	H1 Cell Line	embryonic stem cell
6	chr5:89838600-89839600	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr5:89838600-89841200	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr5:89838800-89839200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
9	chr5:89838800-89839400	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr5:89838800-89839400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
11	chr5:89838800-89839400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr5:89839000-89839200	Enhancers	H9 Cell Line	embryonic stem cell
13	chr5:89839000-89839400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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