Variant report

Variant	rs4602434
Chromosome Location	chr3:121688635-121688636
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:121657236..121660917-chr3:121686314..121690251,4	MCF-7	breast:
2	chr3:121552259..121553812-chr3:121688554..121691121,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC15A2-1	chr3:121685448-121689029	NONHSAT091486

Variant related genes	Relation type
ENSG00000163406	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10470412	1.00[ASW][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];0.92[LWK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs10511407	0.84[ASW][hapmap]
rs12487516	0.81[AFR][1000 genomes]
rs12489686	0.84[ASW][hapmap]
rs12491109	0.84[ASW][hapmap]
rs12492861	1.00[CHB][hapmap]
rs12629720	1.00[CHB][hapmap]
rs13077143	0.94[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13321798	1.00[CHB][hapmap];0.89[GIH][hapmap]
rs1881997	1.00[CHB][hapmap];0.85[GIH][hapmap]
rs1881998	1.00[CHB][hapmap];0.89[GIH][hapmap]
rs1920307	1.00[CHB][hapmap];0.89[GIH][hapmap]
rs1920310	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2293613	1.00[ASW][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2689278	1.00[CHB][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes]
rs2689286	0.81[AFR][1000 genomes]
rs2700413	1.00[CHB][hapmap];0.89[GIH][hapmap]
rs2700414	1.00[CHB][hapmap]
rs2700419	0.86[AFR][1000 genomes]
rs3805132	0.91[AFR][1000 genomes]
rs4603998	0.91[AFR][1000 genomes]
rs4676760	0.91[AFR][1000 genomes]
rs4676761	1.00[ASW][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs55653962	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55955745	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56408673	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438681	1.00[CHB][hapmap]
rs7620562	1.00[CHB][hapmap]
rs7625960	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs7626052	1.00[CHB][hapmap]
rs7650341	1.00[CHB][hapmap];0.89[GIH][hapmap]
rs9834185	1.00[CHB][hapmap]
rs9869891	1.00[CHB][hapmap]
rs9877671	0.91[AFR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33139	chr3:121500400-122091831	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121678800-121693400	Weak transcription	Primary B cells from cord blood	blood
2	chr3:121686000-121698200	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr3:121688200-121689000	Enhancers	HMEC	breast
4	chr3:121688200-121689800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr3:121688400-121689400	Weak transcription	Primary hematopoietic stem cells	blood
6	chr3:121688400-121689800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr3:121688600-121689000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:121688600-121689000	Enhancers	Dnd41	blood
9	chr3:121688600-121689200	Enhancers	Muscle Satellite Cultured Cells	--
10	chr3:121688600-121689200	Enhancers	NHEK	skin
11	chr3:121688600-121689800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr3:121688600-121693200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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