Variant report

Variant	rs2424668
Chromosome Location	chr20:24735946-24735947
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:24726357..24729522-chr20:24732233..24738144,6	MCF-7	breast:

Extended variants
information (count: 68 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11698988	0.82[EUR][1000 genomes]
rs1883922	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2244284	0.88[EUR][1000 genomes]
rs2253628	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs226664	0.88[CEU][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs226667	0.84[EUR][1000 genomes]
rs226668	0.84[EUR][1000 genomes]
rs226669	0.84[EUR][1000 genomes]
rs226670	0.84[EUR][1000 genomes]
rs226671	0.84[EUR][1000 genomes]
rs226672	0.84[EUR][1000 genomes]
rs226674	0.84[EUR][1000 genomes]
rs226675	0.83[EUR][1000 genomes]
rs226676	0.83[EUR][1000 genomes]
rs226677	0.83[EUR][1000 genomes]
rs226678	0.83[EUR][1000 genomes]
rs226679	0.83[EUR][1000 genomes]
rs226680	0.96[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs226681	0.96[CEU][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs226687	0.89[EUR][1000 genomes]
rs226688	0.89[EUR][1000 genomes]
rs226690	0.83[EUR][1000 genomes]
rs226697	0.86[EUR][1000 genomes]
rs226699	0.82[EUR][1000 genomes]
rs2424646	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2424649	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2424650	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2424661	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2424662	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2424663	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2424664	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2424665	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2424666	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2424667	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2424669	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2424670	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2424671	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2424672	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2424673	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2424674	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2424675	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2424678	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4813530	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4815307	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6049931	1.00[ASN][1000 genomes]
rs6049932	1.00[ASN][1000 genomes]
rs6049946	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6049965	0.88[EUR][1000 genomes]
rs6049976	1.00[JPT][hapmap]
rs6049978	1.00[JPT][hapmap]
rs6076275	0.88[EUR][1000 genomes]
rs6076276	0.88[EUR][1000 genomes]
rs6076277	0.86[EUR][1000 genomes]
rs6083620	0.85[EUR][1000 genomes]
rs6106942	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6132765	0.83[EUR][1000 genomes]
rs6138373	0.86[EUR][1000 genomes]
rs85804	0.89[EUR][1000 genomes]
rs971957	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs974647	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24727400-24743400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr20:24732800-24737600	Enhancers	Fetal Thymus	thymus
3	chr20:24733000-24736800	Enhancers	Thymus	Thymus
4	chr20:24734800-24737400	Enhancers	Brain Substantia Nigra	brain
5	chr20:24734800-24737600	Enhancers	Brain Cingulate Gyrus	brain
6	chr20:24735000-24736200	Enhancers	Brain Anterior Caudate	brain
7	chr20:24735000-24736200	Enhancers	Brain Inferior Temporal Lobe	brain
8	chr20:24735000-24737400	Enhancers	Primary hematopoietic stem cells	blood
9	chr20:24735000-24737600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr20:24735000-24737600	Enhancers	Brain Angular Gyrus	brain
11	chr20:24735000-24737600	Enhancers	Brain Hippocampus Middle	brain
12	chr20:24735200-24736000	Enhancers	HepG2	liver
13	chr20:24735200-24736200	Weak transcription	Dnd41	blood
14	chr20:24735200-24736600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr20:24735200-24737000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr20:24735200-24737600	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr20:24735400-24736400	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr20:24735400-24737200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr20:24735400-24737400	Enhancers	Pancreas	Pancrea
20	chr20:24735400-24737800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr20:24735600-24736600	Enhancers	Fetal Kidney	kidney
22	chr20:24735600-24737600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr20:24735600-24737800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr20:24735800-24736200	Weak transcription	Adipose Nuclei	Adipose
25	chr20:24735800-24736800	Enhancers	HSMM	muscle
26	chr20:24735800-24737000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr20:24735800-24737000	Enhancers	HSMMtube	muscle
28	chr20:24735800-24737200	Enhancers	Liver	Liver

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