Variant report

Variant	rs12884884
Chromosome Location	chr14:38014049-38014050
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:38013025..38015360-chr14:38033181..38036117,2	MCF-7	breast:
2	chr14:38011441..38015766-chr14:38062652..38065926,9	MCF-7	breast:
3	chr14:38010426..38020494-chr14:38050537..38062032,33	MCF-7	breast:
4	chr14:38011817..38019831-chr14:38060493..38066722,23	MCF-7	breast:
5	chr14:38012929..38015442-chr14:38030781..38032707,2	MCF-7	breast:
6	chr14:38013523..38020726-chr14:38055776..38060374,10	MCF-7	breast:
7	chr14:38013794..38017816-chr14:38049871..38055560,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000129514	Chromatin interaction
ENSG00000258414	Chromatin interaction
ENSG00000139865	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10133391	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10138614	0.84[YRI][hapmap]
rs10145379	0.82[GIH][hapmap]
rs10145473	0.88[CEU][hapmap];0.89[GIH][hapmap];0.87[TSI][hapmap]
rs10151200	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs10400689	0.89[GIH][hapmap];0.80[TSI][hapmap]
rs11156961	0.88[CEU][hapmap];0.89[GIH][hapmap];0.87[TSI][hapmap]
rs1158700	0.85[EUR][1000 genomes]
rs1158701	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs12147939	0.84[CEU][hapmap]
rs12147950	0.89[ASW][hapmap];0.80[MKK][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes]
rs17768343	0.92[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1884803	0.88[CEU][hapmap];0.89[GIH][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs1950824	0.88[CEU][hapmap];0.89[GIH][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs1950826	0.88[CEU][hapmap];0.89[GIH][hapmap];0.87[TSI][hapmap]
rs1956438	0.85[EUR][1000 genomes]
rs1956439	0.85[EUR][1000 genomes]
rs1956440	0.85[EUR][1000 genomes]
rs1956441	0.91[MEX][hapmap];0.81[MKK][hapmap]
rs1980675	0.88[CEU][hapmap]
rs2038438	0.84[EUR][1000 genomes]
rs2057274	0.82[EUR][1000 genomes]
rs4900958	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.88[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4900966	0.84[EUR][1000 genomes]
rs4900967	0.83[EUR][1000 genomes]
rs4900969	0.88[CEU][hapmap];0.87[GIH][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs4900972	0.82[EUR][1000 genomes]
rs7143956	0.84[EUR][1000 genomes]
rs7144658	0.82[GIH][hapmap]
rs7159456	0.88[CEU][hapmap];0.89[GIH][hapmap];0.87[TSI][hapmap]
rs7493775	0.88[CEU][hapmap];0.89[GIH][hapmap];0.87[TSI][hapmap]
rs8005136	0.80[CEU][hapmap];0.85[GIH][hapmap];0.84[TSI][hapmap]
rs981794	0.91[MEX][hapmap];0.81[MKK][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530038	chr14:37590543-38336191	Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv901639	chr14:37743583-38038468	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv564349	chr14:37890433-38034434	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv901641	chr14:37939401-38040755	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12884884	TRAPPC6B	cis	cerebellum	SCAN
rs12884884	BRMS1L	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:38008000-38021000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr14:38008200-38017800	Weak transcription	Aorta	Aorta
3	chr14:38010800-38016000	Weak transcription	Left Ventricle	heart
4	chr14:38013600-38014600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr14:38013600-38015600	Enhancers	HepG2	liver
6	chr14:38013800-38014200	Enhancers	Liver	Liver
7	chr14:38013800-38021200	Weak transcription	Right Ventricle	heart
8	chr14:38013800-38023200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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