Variant report

Variant	rs648430
Chromosome Location	chr5:89828258-89828259
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:89826684..89828882-chr5:89853247..89854802,2	K562	blood:
2	chr5:89825899..89828736-chr5:89905925..89909224,3	K562	blood:
3	chr5:89708413..89711602-chr5:89825612..89828655,3	K562	blood:
4	chr5:89766469..89774126-chr5:89823341..89829105,11	K562	blood:
5	chr5:89823946..89826713-chr5:89827951..89830249,2	MCF-7	breast:
6	chr5:89826971..89828828-chr5:89846994..89849813,2	MCF-7	breast:
7	chr5:89826199..89831045-chr5:89834037..89838315,7	K562	blood:
8	chr5:89825598..89829055-chr5:89851441..89854747,4	K562	blood:
9	chr5:89768855..89773751-chr5:89822671..89829297,12	K562	blood:
10	chr5:89827458..89830641-chr5:89851988..89854819,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000176055	Chromatin interaction
ENSG00000113356	Chromatin interaction
ENSG00000176018	Chromatin interaction
ENSG00000164199	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10036980	0.85[JPT][hapmap]
rs10043836	0.85[JPT][hapmap]
rs10058765	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs10060427	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs10062714	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs10062924	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs10067181	0.85[JPT][hapmap]
rs10068473	0.85[JPT][hapmap]
rs10072105	0.81[CHB][hapmap];0.92[JPT][hapmap]
rs1028191	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs1028192	0.85[JPT][hapmap]
rs1033290	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs10462342	0.82[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap]
rs10473936	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1047787	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10514327	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10514333	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs10942596	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs10942597	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10942605	0.85[JPT][hapmap]
rs10942606	0.85[JPT][hapmap]
rs1160121	0.85[JPT][hapmap]
rs11741740	0.81[ASN][1000 genomes]
rs11743030	0.81[CHB][hapmap]
rs12188928	0.85[JPT][hapmap]
rs12516985	0.83[JPT][hapmap]
rs12655180	0.80[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13182165	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13185955	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1533603	0.85[JPT][hapmap]
rs1673378	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1673379	0.92[JPT][hapmap]
rs16868957	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs1700510	0.96[CEU][hapmap];0.81[CHB][hapmap];0.83[JPT][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1700511	0.92[JPT][hapmap]
rs1812737	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1878878	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs1993474	0.84[JPT][hapmap]
rs2176624	0.85[JPT][hapmap]
rs2222242	0.85[JPT][hapmap]
rs2366771	0.81[CHB][hapmap];0.92[JPT][hapmap]
rs2366773	0.92[JPT][hapmap]
rs2366774	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs2366777	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs3087840	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35407205	0.84[ASN][1000 genomes]
rs3805483	1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[MEX][hapmap];0.84[ASN][1000 genomes]
rs474800	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs490812	0.92[JPT][hapmap]
rs4916681	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs4916684	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs4916686	0.85[JPT][hapmap]
rs4916813	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs4916815	0.83[JPT][hapmap]
rs498491	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs499148	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs501640	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs502596	0.92[JPT][hapmap]
rs552314	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs558809	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs587818	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs603015	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs603870	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs616379	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs617379	0.81[CHB][hapmap];0.92[JPT][hapmap]
rs618355	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs623761	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs637442	0.92[JPT][hapmap]
rs6452906	0.85[JPT][hapmap]
rs645652	0.81[CHB][hapmap];0.82[CHD][hapmap];0.92[JPT][hapmap]
rs666659	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67376567	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6863710	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs6878917	0.81[CHB][hapmap];0.92[JPT][hapmap]
rs6881412	0.85[JPT][hapmap]
rs6883872	0.92[JPT][hapmap]
rs6888355	0.85[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs688956	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs688960	0.81[CHB][hapmap];0.92[JPT][hapmap]
rs6897910	1.00[CEU][hapmap];0.93[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6898209	0.85[JPT][hapmap]
rs7703588	0.85[JPT][hapmap]
rs7716979	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7717423	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7721198	0.82[JPT][hapmap]
rs7723259	0.84[JPT][hapmap]
rs7724806	0.85[JPT][hapmap]
rs7726624	0.81[CHB][hapmap];0.92[JPT][hapmap]
rs7729703	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs7732169	0.85[JPT][hapmap]
rs9293550	0.85[JPT][hapmap]
rs963866	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs977906	0.85[JPT][hapmap]
rs9790907	0.81[CHB][hapmap];0.92[JPT][hapmap]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs648430	LYSMD3	cis	normal skin	skin_eQTL
rs648430	GPR98	cis	cerebellum	SCAN
rs648430	LYSMD3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:11 , 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	chr5:89826600-89831000	Weak transcription	Fetal Intestine Small	intestine
3	chr5:89826600-89831200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr5:89826600-89833000	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr5:89826600-89833400	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr5:89826800-89843200	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr5:89827000-89829600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr5:89827000-89829800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr5:89827200-89829200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr5:89827400-89829600	Weak transcription	K562	blood
11	chr5:89827600-89831000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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