Variant report

Variant	rs10467951
Chromosome Location	chr15:76023721-76023722
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:76021238..76025261-chr15:76028458..76030884,3	MCF-7	breast:
2	chr15:76019014..76021554-chr15:76023270..76025414,2	MCF-7	breast:
3	chr15:76012704..76015019-chr15:76022800..76024419,2	MCF-7	breast:
4	chr15:76022261..76024387-chr15:76088490..76090434,2	MCF-7	breast:
5	chr15:76021736..76024634-chr15:76026770..76028436,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260288	Chromatin interaction
ENSG00000256530	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10851883	0.92[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap]
rs12594714	0.92[CEU][hapmap]
rs12908447	0.92[CEU][hapmap]
rs2255254	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2255269	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2405895	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2405897	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2405898	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2405902	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2593286	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2593293	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2593298	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2604411	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2675216	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2675217	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2675220	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4886456	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4886458	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4886735	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4886953	0.83[EUR][1000 genomes]
rs749161	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8032669	0.89[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3445070	chr15:75623136-76045948	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
2	nsv531903	chr15:75889302-76342128	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
3	nsv527186	chr15:75924443-76107730	Active TSS Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	69 gene(s)	inside rSNPs	diseases
4	nsv904392	chr15:75930757-76039262	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
5	nsv904394	chr15:75948671-76039262	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv904396	chr15:75961518-76071105	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs10467951	CSK	cis	cerebellum	SCAN
rs10467951	NRG4	cis	cerebellum	SCAN
rs10467951	ARID3B	cis	cerebellum	SCAN
rs10467951	NRG4	cis	parietal	SCAN
rs10467951	TRAPPC9	trans	parietal	SCAN
rs10467951	C15orf59	cis	parietal	SCAN
rs10467951	ETFA	cis	parietal	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76013600-76025000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr15:76013800-76029800	Weak transcription	HSMM	muscle
3	chr15:76016600-76023800	Weak transcription	Ovary	ovary
4	chr15:76016600-76024000	Weak transcription	Brain Germinal Matrix	brain
5	chr15:76016800-76023800	Weak transcription	Right Ventricle	heart
6	chr15:76016800-76025200	Weak transcription	Pancreas	Pancrea
7	chr15:76018800-76023800	Weak transcription	Fetal Heart	heart
8	chr15:76018800-76024400	Weak transcription	Left Ventricle	heart
9	chr15:76019800-76023800	Weak transcription	Placenta	Placenta
10	chr15:76020000-76025000	Weak transcription	Esophagus	oesophagus
11	chr15:76020200-76025200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr15:76020600-76030200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr15:76020800-76024000	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr15:76020800-76026400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr15:76021000-76023800	Weak transcription	Stomach Smooth Muscle	stomach
16	chr15:76021000-76024200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr15:76021000-76030200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr15:76021000-76030200	Weak transcription	HMEC	breast
19	chr15:76021400-76023800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr15:76021400-76029600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr15:76021600-76023800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr15:76022000-76028800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr15:76022800-76023800	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr15:76023000-76026000	Enhancers	Fetal Muscle Trunk	muscle
25	chr15:76023200-76023800	Weak transcription	Spleen	Spleen
26	chr15:76023400-76024200	Enhancers	Fetal Stomach	stomach
27	chr15:76023400-76025600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr15:76023600-76023800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr15:76023600-76023800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr15:76023600-76023800	Enhancers	Brain Angular Gyrus	brain
31	chr15:76023600-76023800	Enhancers	Colon Smooth Muscle	Colon
32	chr15:76023600-76023800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
33	chr15:76023600-76023800	Enhancers	Rectal Smooth Muscle	rectum
34	chr15:76023600-76024000	Enhancers	Adipose Nuclei	Adipose
35	chr15:76023600-76024200	Enhancers	Fetal Intestine Small	intestine
36	chr15:76023600-76024200	Enhancers	Lung	lung
37	chr15:76023600-76024400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr15:76023600-76025000	Enhancers	Rectal Mucosa Donor 29	rectum
39	chr15:76023600-76025200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr15:76023600-76025400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr15:76023600-76025400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
42	chr15:76023600-76025400	Flanking Active TSS	Fetal Lung	lung
43	chr15:76023600-76025600	Enhancers	Duodenum Smooth Muscle	Duodenum
44	chr15:76023600-76025600	Enhancers	Fetal Thymus	thymus
45	chr15:76023600-76025800	Enhancers	Fetal Muscle Leg	muscle

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