Variant report

Variant	rs6138373
Chromosome Location	chr20:24755469-24755470
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:24749036..24750576-chr20:24754349..24756115,2	MCF-7	breast:
2	chr20:24633208..24634877-chr20:24753642..24755749,2	MCF-7	breast:

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs11698988	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1883922	0.94[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs2244284	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2253628	0.86[EUR][1000 genomes]
rs226664	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs226667	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs226668	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs226669	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs226670	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs226671	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs226672	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs226674	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs226675	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs226676	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs226677	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs226678	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs226679	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs226680	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs226681	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs226687	0.84[EUR][1000 genomes]
rs226688	0.83[EUR][1000 genomes]
rs226690	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs226697	0.80[EUR][1000 genomes]
rs226699	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2424646	0.94[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs2424649	0.93[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs2424650	0.86[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs2424661	0.86[EUR][1000 genomes]
rs2424662	0.98[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs2424663	0.86[EUR][1000 genomes]
rs2424664	0.86[EUR][1000 genomes]
rs2424665	0.86[EUR][1000 genomes]
rs2424666	0.86[EUR][1000 genomes]
rs2424667	0.86[EUR][1000 genomes]
rs2424668	0.86[EUR][1000 genomes]
rs2424669	0.98[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs2424670	0.84[EUR][1000 genomes]
rs2424671	0.85[EUR][1000 genomes]
rs2424672	0.85[EUR][1000 genomes]
rs2424673	0.85[EUR][1000 genomes]
rs2424674	0.98[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs2424675	0.85[EUR][1000 genomes]
rs2424678	0.98[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs2424689	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4813530	0.93[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs4813538	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs4813539	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs4815307	0.85[EUR][1000 genomes]
rs6049946	0.86[EUR][1000 genomes]
rs6049965	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6076275	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6076276	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6076277	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6083620	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6106942	0.98[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs6114868	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6132765	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs85804	0.84[EUR][1000 genomes]
rs971957	0.94[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs974647	0.91[AFR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3332519	chr20:24535099-24815615	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1061412	chr20:24629468-24887869	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv544216	chr20:24629468-24887869	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1061281	chr20:24711635-24815107	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv544217	chr20:24711635-24815107	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv912825	chr20:24715544-24813345	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv1061455	chr20:24733120-24861801	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv544218	chr20:24733120-24861801	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv1059270	chr20:24741923-24787243	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	Chromatin interactive region	2 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	chr20:24745400-24755600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr20:24749200-24763600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr20:24751000-24761200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr20:24753400-24755600	Enhancers	Osteobl	bone
5	chr20:24753400-24761200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr20:24754400-24755600	Enhancers	NH-A	brain
7	chr20:24754400-24758600	Weak transcription	Fetal Muscle Leg	muscle
8	chr20:24755000-24757800	Weak transcription	Fetal Thymus	thymus
9	chr20:24755000-24758800	Weak transcription	Thymus	Thymus
10	chr20:24755200-24757000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr20:24755400-24756800	Weak transcription	NHEK	skin
12	chr20:24755400-24757000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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