Variant report

Variant	rs1003219
Chromosome Location	chr5:59164993-59164994
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1003218	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10042020	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10066777	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10514880	0.92[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10514888	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs13186506	1.00[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs1369286	1.00[CEU][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs154144	0.86[ASN][1000 genomes]
rs159608	0.84[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs159610	0.86[ASN][1000 genomes]
rs159622	0.84[CHB][hapmap];0.86[ASN][1000 genomes]
rs159624	0.84[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs159626	0.86[ASN][1000 genomes]
rs16890200	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs16890226	1.00[CHB][hapmap]
rs16890228	1.00[CHB][hapmap]
rs16890269	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16890276	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16890316	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs173945	0.84[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs17742850	0.88[CEU][hapmap]
rs17799450	0.88[CEU][hapmap];0.92[GIH][hapmap];1.00[TSI][hapmap]
rs181924	0.86[ASN][1000 genomes]
rs256348	0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs256350	0.84[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs256353	0.84[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs6859121	1.00[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6868846	0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs6889984	1.00[CEU][hapmap];0.84[CHB][hapmap];0.83[CHD][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.83[YRI][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018015	chr5:58889470-59532667	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv537766	chr5:58889470-59532667	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv534614	chr5:58962510-59388525	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1003219	MSX1	trans	lymphoblastoid	seeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59160000-59165000	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr5:59160800-59165000	Weak transcription	HSMMtube	muscle
3	chr5:59160800-59189000	Weak transcription	Aorta	Aorta
4	chr5:59161600-59165000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr5:59163200-59168600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr5:59163600-59166000	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr5:59164200-59165000	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr5:59164400-59165600	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr5:59164400-59165600	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr5:59164600-59165600	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr5:59164800-59165000	Weak transcription	Brain Germinal Matrix	brain
12	chr5:59164800-59165600	Enhancers	H9 Cell Line	embryonic stem cell
13	chr5:59164800-59165600	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr5:59164800-59172000	Enhancers	HSMM	muscle

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