Variant report

Variant	rs1991573
Chromosome Location	chr10:43541016-43541017
allele	G/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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:43540474..43542331-chr10:43555929..43558160,2	MCF-7	breast:
2	chr10:43531524..43548583-chr10:43564333..43580527,54	MCF-7	breast:
3	chr10:43539137..43541120-chr10:43541349..43544216,2	K562	blood:
4	chr10:43538130..43541758-chr10:43570526..43575204,4	MCF-7	breast:
5	chr10:43540640..43543554-chr10:43558547..43560903,3	MCF-7	breast:
6	chr10:43539819..43542010-chr10:43547836..43549508,2	MCF-7	breast:
7	chr10:43537183..43538884-chr10:43539008..43541736,2	MCF-7	breast:
8	chr10:43539794..43541332-chr10:43557128..43559148,2	MCF-7	breast:
9	chr10:43540789..43543253-chr10:43544973..43547558,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000165731	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1109750	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11239865	0.93[ASN][1000 genomes]
rs1254987	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1254988	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1268630	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1891450	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2082106	0.90[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];0.83[JPT][hapmap];0.92[ASN][1000 genomes]
rs2115816	0.93[ASN][1000 genomes]
rs2256432	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2488279	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2488280	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2488282	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2506038	1.00[YRI][hapmap]
rs2565191	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2995399	0.95[CHB][hapmap];0.81[AMR][1000 genomes]
rs3026698	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3097565	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3097566	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3123715	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3128737	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3128739	0.94[CEU][hapmap]
rs3128740	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs731732	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050394	chr10:42890663-43604956	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv540573	chr10:42890663-43604956	Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
3	nsv534548	chr10:42890664-43729688	Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv430159	chr10:43291894-43946294	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
5	nsv1038102	chr10:43441601-43642908	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv466880	chr10:43452436-43616751	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
7	nsv550695	chr10:43452436-43616751	Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
8	nsv895080	chr10:43471575-43558757	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
9	nsv895082	chr10:43530071-43755506	Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1991573	CSGALNACT2	cis	parietal	SCAN
rs1991573	ALOX5	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43538600-43542400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr10:43539600-43541800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr10:43540200-43541400	Weak transcription	Fetal Lung	lung
4	chr10:43540200-43544000	Weak transcription	Placenta	Placenta
5	chr10:43540200-43556600	Weak transcription	Spleen	Spleen
6	chr10:43540400-43541400	Weak transcription	Primary hematopoietic stem cells	blood
7	chr10:43540400-43541400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr10:43540400-43542400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr10:43540400-43547600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr10:43540600-43541400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr10:43540600-43544400	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr10:43540600-43544600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr10:43540800-43541800	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr10:43540800-43541800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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