Variant report

Variant	rs7176579
Chromosome Location	chr15:51464187-51464188
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:76140334..76142317-chr15:51462665..51465523,2	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1025738	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1025739	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10519293	0.96[ASN][1000 genomes]
rs1075680	0.94[ASW][hapmap];0.86[CHB][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];0.83[MKK][hapmap];0.81[TSI][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11070838	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1122044	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12323970	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12324478	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12324672	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12442450	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12898341	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12904155	0.82[JPT][hapmap]
rs12904416	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12907367	0.82[JPT][hapmap]
rs12915091	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1438926	0.82[JPT][hapmap]
rs16964048	0.88[JPT][hapmap]
rs16964113	0.81[ASN][1000 genomes]
rs2118784	0.85[AFR][1000 genomes]
rs2278559	0.88[JPT][hapmap]
rs35665801	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4775922	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56039974	0.81[ASN][1000 genomes]
rs56140513	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58099273	0.81[ASN][1000 genomes]
rs7170009	0.82[JPT][hapmap]
rs745258	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8040954	0.88[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047443	chr15:50744781-51647023	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	nsv569399	chr15:50874964-51562198	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
3	nsv569400	chr15:50874964-51767265	ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
4	nsv904214	chr15:51204364-51535192	Strong transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1049644	chr15:51265447-51560445	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	esv34532	chr15:51276128-51752856	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised 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	21 gene(s)	inside rSNPs	diseases
7	esv2758382	chr15:51282257-51830339	Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	esv2760031	chr15:51282257-51830339	Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv471243	chr15:51345485-52018096	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
10	esv2757600	chr15:51352249-51783981	Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7176579	SQRDL	cis	parietal	SCAN
rs7176579	TNFAIP8L3	cis	parietal	SCAN
rs7176579	HDC	cis	parietal	SCAN
rs7176579	SHC4	cis	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51463000-51464200	Enhancers	Aorta	Aorta
2	chr15:51463000-51464600	Enhancers	Right Atrium	heart
3	chr15:51463000-51464600	Enhancers	Right Ventricle	heart
4	chr15:51463000-51465200	Enhancers	Fetal Brain Male	brain
5	chr15:51463200-51464200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr15:51463200-51464200	Enhancers	Placenta	Placenta
7	chr15:51463200-51464400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr15:51463200-51464800	Enhancers	Fetal Muscle Leg	muscle
9	chr15:51463200-51465600	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr15:51463400-51464200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr15:51463600-51464200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr15:51463600-51464200	Enhancers	NHDF-Ad	bronchial
13	chr15:51463600-51464200	Enhancers	Osteobl	bone
14	chr15:51463600-51464400	Flanking Active TSS	Fetal Heart	heart
15	chr15:51463600-51464400	Enhancers	Skeletal Muscle Female	skeletal muscle
16	chr15:51463600-51464600	Enhancers	Ovary	ovary
17	chr15:51463600-51464800	Enhancers	HSMMtube	muscle
18	chr15:51463800-51464200	Enhancers	Brain Anterior Caudate	brain
19	chr15:51463800-51464200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
20	chr15:51463800-51464200	Enhancers	Fetal Lung	lung
21	chr15:51463800-51464400	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr15:51463800-51464400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr15:51463800-51464400	Enhancers	Fetal Stomach	stomach
24	chr15:51463800-51464400	Enhancers	NHLF	lung
25	chr15:51463800-51464600	Enhancers	Liver	Liver
26	chr15:51463800-51464600	Flanking Active TSS	Stomach Smooth Muscle	stomach
27	chr15:51463800-51464800	Enhancers	Colon Smooth Muscle	Colon
28	chr15:51463800-51465000	Enhancers	Fetal Brain Female	brain
29	chr15:51463800-51465400	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr15:51463800-51465600	Enhancers	Monocytes-CD14+_RO01746	blood
31	chr15:51464000-51464200	Enhancers	Rectal Smooth Muscle	rectum
32	chr15:51464000-51464400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr15:51464000-51464800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr15:51464000-51464800	Bivalent Enhancer	HUVEC	blood vessel
35	chr15:51464000-51465000	Enhancers	Muscle Satellite Cultured Cells	--
36	chr15:51464000-51465000	Weak transcription	Fetal Muscle Trunk	muscle
37	chr15:51464000-51465000	Enhancers	HSMM	muscle
38	chr15:51464000-51465400	Weak transcription	Brain Substantia Nigra	brain
39	chr15:51464000-51465400	Weak transcription	Left Ventricle	heart
40	chr15:51464000-51477000	Weak transcription	Gastric	stomach

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