Variant report

Variant	rs10178396
Chromosome Location	chr2:113699055-113699056
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:113694655..113699559-chr2:113699730..113703257,4	MCF-7	breast:
2	chr2:113642230..113643259-chr2:113698990..113700080,4	MCF-7	breast:
3	chr2:113506923..113507895-chr2:113698818..113699884,5	MCF-7	breast:
4	chr2:113506982..113507851-chr2:113699030..113699972,2	K562	blood:
5	chr2:113031587..113033869-chr2:113697518..113699436,2	K562	blood:
6	chr2:113649179..113649918-chr2:113699043..113699938,2	MCF-7	breast:
7	chr2:113357284..113358273-chr2:113699007..113699673,4	K562	blood:

Variant related genes	Relation type
ENSG00000188177	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10188477	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10188765	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10199311	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10206205	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10221977	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10864907	0.92[CEU][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10864908	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11123153	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11123154	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11674086	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11683383	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11690399	0.85[CEU][hapmap];0.90[GIH][hapmap];0.83[MEX][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11695077	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11893071	0.91[ASN][1000 genomes]
rs11897907	0.85[CEU][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12468164	0.96[ASN][1000 genomes]
rs12471839	0.91[ASN][1000 genomes]
rs12617864	0.90[ASN][1000 genomes]
rs12711745	0.98[ASN][1000 genomes]
rs12987491	0.90[ASN][1000 genomes]
rs13029531	0.85[CEU][hapmap];0.90[GIH][hapmap];0.87[MEX][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13029703	0.83[CEU][hapmap];0.81[CHB][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2068777	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2708931	0.86[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs2708932	0.90[ASN][1000 genomes]
rs2723163	0.95[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2723197	0.81[ASN][1000 genomes]
rs4077216	0.92[ASN][1000 genomes]
rs4254516	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4387792	0.83[ASN][1000 genomes]
rs4538207	0.98[ASN][1000 genomes]
rs4848309	0.83[ASN][1000 genomes]
rs6716380	0.91[ASN][1000 genomes]
rs6723582	0.91[ASN][1000 genomes]
rs6735589	0.90[ASN][1000 genomes]
rs6747618	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7557537	0.98[ASN][1000 genomes]
rs7559466	0.81[CEU][hapmap];0.80[JPT][hapmap]
rs879710	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs879711	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[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	nsv532471	chr2:113682449-113862981	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv997348	chr2:113688093-113986508	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv979388	chr2:113696105-113705504	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10178396	DPP10	cis	parietal	SCAN
rs10178396	ACOXL	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113694000-113699200	Weak transcription	Primary monocytes fromperipheralblood	blood
2	chr2:113697000-113699800	Enhancers	Liver	Liver
3	chr2:113697200-113699400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr2:113697400-113699200	Weak transcription	HMEC	breast
5	chr2:113697400-113699400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr2:113697400-113699600	Weak transcription	Gastric	stomach
7	chr2:113697600-113699400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr2:113697600-113700400	Enhancers	Colon Smooth Muscle	Colon
9	chr2:113698200-113699800	Enhancers	Rectal Smooth Muscle	rectum
10	chr2:113698200-113700000	Enhancers	Stomach Mucosa	stomach
11	chr2:113699000-113699600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr2:113699000-113699800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr2:113699000-113700800	Enhancers	NHEK	skin
14	chr2:113699000-113701000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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