Variant report

Variant	rs175299
Chromosome Location	chr20:15215964-15215965
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	chr20:14857662..14859546-chr20:15214980..15217486,2	MCF-7	breast:
2	chr20:14316387..14318274-chr20:15215878..15217670,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000125848	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs175259	0.87[ASW][hapmap];0.84[LWK][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes]
rs175264	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs175270	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs175271	0.85[ASN][1000 genomes]
rs175272	0.87[ASN][1000 genomes]
rs175274	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs175275	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs175276	1.00[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap];0.88[TSI][hapmap];0.85[ASN][1000 genomes]
rs175279	1.00[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap];0.88[TSI][hapmap];0.83[ASN][1000 genomes]
rs175280	0.85[ASN][1000 genomes]
rs175281	0.85[ASN][1000 genomes]
rs175282	0.85[ASN][1000 genomes]
rs175285	1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs175286	0.83[ASN][1000 genomes]
rs175287	0.84[ASN][1000 genomes]
rs175288	0.87[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs175289	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs175290	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs175291	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs175296	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs175297	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs175298	0.81[YRI][hapmap]
rs175300	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs175301	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs175302	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs175303	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs175304	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs175307	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs175308	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.91[ASN][1000 genomes]
rs175309	0.91[ASN][1000 genomes]
rs175310	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.91[ASN][1000 genomes]
rs175311	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.91[ASN][1000 genomes]
rs175312	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.91[ASN][1000 genomes]
rs175313	0.91[ASN][1000 genomes]
rs175314	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs175315	0.88[ASN][1000 genomes]
rs175316	0.91[ASN][1000 genomes]

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	nsv1065152	chr20:14781684-15305258	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv585540	chr20:14858910-15242365	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1062252	chr20:14964258-15547739	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv544206	chr20:14964258-15547739	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv524481	chr20:15007730-15382919	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv916795	chr20:15041479-15345528	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv1060275	chr20:15084485-15327541	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv526767	chr20:15086277-15223632	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv1058827	chr20:15159151-15289719	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	nsv1058629	chr20:15211386-15252831	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	esv3348430	chr20:15214002-15216300	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:15202200-15217400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr20:15215800-15217800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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