Variant report

Variant	rs4598846
Chromosome Location	chr15:51388115-51388116
allele	A/G
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	chr15:51374735..51377659-chr15:51385754..51389535,3	MCF-7	breast:
2	chr15:51385109..51388329-chr15:51394430..51396679,3	MCF-7	breast:
3	chr15:51383701..51385966-chr15:51387916..51389440,2	K562	blood:
4	chr15:51386847..51389829-chr15:51423668..51425272,2	MCF-7	breast:
5	chr15:51387979..51389847-chr15:51401200..51403539,2	K562	blood:
6	chr15:51383701..51385814-chr15:51386600..51389440,2	K562	blood:
7	chr15:51387867..51389952-chr15:51399669..51401269,2	MCF-7	breast:
8	chr15:51385170..51388153-chr15:51390424..51392777,2	K562	blood:
9	chr15:51199017..51202160-chr15:51384905..51388253,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000081014	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1009882	0.81[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs11070822	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs11070831	0.83[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap]
rs11070832	0.83[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap]
rs11070833	0.88[ASN][1000 genomes]
rs11070834	0.83[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1124769	0.95[CHB][hapmap];0.82[CHD][hapmap];0.89[JPT][hapmap]
rs1135397	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs12442459	0.95[CHB][hapmap];0.93[JPT][hapmap]
rs12443062	0.84[ASN][1000 genomes]
rs12591434	0.95[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs12591500	0.82[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap]
rs12591735	0.83[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs12592941	0.90[ASN][1000 genomes]
rs12593342	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs12593764	0.82[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.89[JPT][hapmap]
rs12593778	0.82[CEU][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];0.89[JPT][hapmap]
rs12595526	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs12595551	0.80[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs12595600	0.83[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs12909470	0.81[ASN][1000 genomes]
rs12911168	0.93[ASN][1000 genomes]
rs12912106	0.86[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap]
rs12914185	0.83[CEU][hapmap];0.90[CHB][hapmap]
rs12916845	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs17647040	0.83[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs17703518	0.81[ASN][1000 genomes]
rs1876784	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs1904430	0.91[CHB][hapmap]
rs2291107	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs2614793	0.91[CHB][hapmap];0.88[JPT][hapmap]
rs2663542	0.95[CHB][hapmap];0.83[JPT][hapmap]
rs28637301	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34013374	0.81[ASN][1000 genomes]
rs3784304	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs3825798	0.83[CEU][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];0.89[JPT][hapmap]
rs4304967	0.94[ASN][1000 genomes]
rs56036336	0.94[ASN][1000 genomes]
rs7170455	0.83[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs7177664	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72727114	0.84[ASN][1000 genomes]
rs72727115	0.84[ASN][1000 genomes]
rs8182062	0.96[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap]
rs936482	0.95[CHB][hapmap];0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv428634	chr15:51299632-51446666	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	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
11	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4598846	SHF	cis	parietal	SCAN
rs4598846	LYSMD2	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51385600-51388400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr15:51385800-51388200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
3	chr15:51387400-51388200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr15:51387400-51388200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr15:51387400-51388200	Weak transcription	Spleen	Spleen
6	chr15:51387600-51388200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr15:51387600-51388400	Flanking Active TSS	HUVEC	blood vessel
8	chr15:51387800-51388200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr15:51387800-51388200	Enhancers	Ovary	ovary
10	chr15:51387800-51388200	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
11	chr15:51387800-51389200	Weak transcription	HMEC	breast
12	chr15:51387800-51390400	Weak transcription	Lung	lung
13	chr15:51387800-51390800	Enhancers	HepG2	liver
14	chr15:51387800-51393000	Weak transcription	Esophagus	oesophagus
15	chr15:51388000-51388200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
16	chr15:51388000-51388200	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
17	chr15:51388000-51388200	Enhancers	Muscle Satellite Cultured Cells	--
18	chr15:51388000-51388200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr15:51388000-51388200	Bivalent Enhancer	Fetal Heart	heart
20	chr15:51388000-51388400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr15:51388000-51388400	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr15:51388000-51389200	Weak transcription	HSMM	muscle
23	chr15:51388000-51389200	Weak transcription	HSMMtube	muscle
24	chr15:51388000-51389400	Weak transcription	Brain Hippocampus Middle	brain
25	chr15:51388000-51389800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr15:51388000-51390000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr15:51388000-51396000	Weak transcription	Aorta	Aorta

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