Variant report

Variant	rs10003459
Chromosome Location	chr4:159016754-159016755
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:159015350..159017695-chr4:159032159..159035060,3	MCF-7	breast:
2	chr4:159013562..159016824-chr4:159081048..159085392,5	MCF-7	breast:
3	chr4:159013245..159018298-chr4:159091169..159093561,5	MCF-7	breast:
4	chr4:158999977..159001907-chr4:159015596..159017167,2	MCF-7	breast:
5	chr4:158912571..158916849-chr4:159013907..159018478,8	MCF-7	breast:
6	chr4:159010029..159020346-chr4:159088735..159099117,18	MCF-7	breast:
7	chr4:158912471..158914570-chr4:159016207..159019038,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164125	Chromatin interaction
ENSG00000248429	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10003566	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10005547	0.83[EUR][1000 genomes]
rs10005656	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10005901	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10027000	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10049927	0.96[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap]
rs11100149	0.83[EUR][1000 genomes]
rs12503001	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13106004	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13106234	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13126694	0.81[CHB][hapmap]
rs28477319	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28514324	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34237515	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4077776	0.96[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap]
rs4362869	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4388135	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4487405	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4513617	0.83[EUR][1000 genomes]
rs4574459	0.92[CEU][hapmap];0.88[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs4631100	0.92[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap]
rs4691452	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4691460	0.94[CHB][hapmap];0.87[CHD][hapmap]
rs6536298	0.85[CEU][hapmap];0.82[CHD][hapmap];0.83[EUR][1000 genomes]
rs6814979	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap]
rs6830475	0.94[CHB][hapmap];0.87[CHD][hapmap]
rs6833295	0.92[CEU][hapmap];0.94[CHB][hapmap]
rs6843728	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6844184	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6848159	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7656059	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7657303	0.96[CEU][hapmap];0.88[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs7692254	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap]
rs9968557	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9993747	0.83[EUR][1000 genomes]
rs9995402	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv993476	chr4:158550643-159202015	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1030124	chr4:158758675-159251140	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv881288	chr4:158891733-159028080	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv1021067	chr4:158972282-159175475	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv880293	chr4:159012365-159049020	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10003459	DKFZp434L142	cis	multi-tissue	Pritchard
rs10003459	FAM198B	cis	Whole Blood	GTEx

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:159014200-159016800	Enhancers	Placenta Amnion	Placenta Amnion
2	chr4:159014200-159017000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr4:159014400-159017200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr4:159014600-159016800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr4:159014600-159017000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr4:159014600-159017000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr4:159015000-159016800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr4:159015000-159017000	Enhancers	NH-A	brain
9	chr4:159015400-159016800	Enhancers	HUVEC	blood vessel
10	chr4:159015400-159017000	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr4:159015400-159017000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr4:159016000-159017000	Enhancers	HMEC	breast
13	chr4:159016200-159016800	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr4:159016200-159017000	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr4:159016200-159020400	Weak transcription	HepG2	liver
16	chr4:159016400-159017000	Enhancers	Ovary	ovary
17	chr4:159016400-159017000	Enhancers	NHEK	skin
18	chr4:159016400-159024000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr4:159016600-159017000	Enhancers	A549	lung

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