Variant report

Variant	rs10043135
Chromosome Location	chr5:96439797-96439798
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:96438791..96440581-chr5:96475884..96478503,2	K562	blood:

Variant related genes	Relation type
ENSG00000145721	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10039917	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10071737	0.96[ASN][1000 genomes]
rs1035507	0.98[ASN][1000 genomes]
rs10463198	0.85[CHB][hapmap];0.92[CHD][hapmap];0.84[JPT][hapmap]
rs11954059	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11958159	0.85[CEU][hapmap];0.91[TSI][hapmap]
rs12520374	0.94[ASN][1000 genomes]
rs13167790	0.95[ASN][1000 genomes]
rs182625	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2287903	0.98[ASN][1000 genomes]
rs2544769	0.95[CHB][hapmap];0.86[ASN][1000 genomes]
rs2544776	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs316178	0.96[ASN][1000 genomes]
rs316190	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316201	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs316202	0.94[ASN][1000 genomes]
rs316203	0.95[ASN][1000 genomes]
rs316204	0.95[ASN][1000 genomes]
rs316205	0.95[ASN][1000 genomes]
rs316207	0.89[CHD][hapmap]
rs316209	0.89[CHD][hapmap];0.84[JPT][hapmap]
rs316213	0.85[CHB][hapmap];0.92[CHD][hapmap];0.84[JPT][hapmap]
rs316217	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs316218	0.97[ASN][1000 genomes]
rs316219	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs316223	0.84[ASN][1000 genomes]
rs316224	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs316232	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs316233	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs316234	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs389536	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs392723	0.81[ASN][1000 genomes]
rs444243	0.97[ASN][1000 genomes]
rs6556945	0.84[ASN][1000 genomes]
rs7717829	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[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	nsv432755	chr5:95987984-96657483	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv598962	chr5:96057891-96893164	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv830412	chr5:96427305-96606619	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10043135	LIX1	cis	parietal	SCAN
rs10043135	MYO7B	trans	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:96428400-96440000	Weak transcription	K562	blood
2	chr5:96432800-96445600	Weak transcription	Primary B cells from cord blood	blood
3	chr5:96435000-96447400	Weak transcription	Fetal Muscle Leg	muscle
4	chr5:96437200-96441400	Strong transcription	Primary B cells from peripheral blood	blood
5	chr5:96437600-96441800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr5:96438000-96441600	Weak transcription	Colon Smooth Muscle	Colon
7	chr5:96438200-96440800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr5:96438200-96440800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr5:96438200-96441800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr5:96438200-96442000	Weak transcription	Fetal Stomach	stomach
11	chr5:96438400-96441800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr5:96438400-96443600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr5:96438600-96440000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr5:96438600-96442000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr5:96438600-96454800	Weak transcription	Brain Hippocampus Middle	brain
16	chr5:96439200-96441800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr5:96439600-96440000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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