Variant report

Variant	rs2424681
Chromosome Location	chr20:24748829-24748830
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	chr20:24746739..24748935-chr20:24753285..24754881,2	MCF-7	breast:

Extended variants
information (count: 110 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs1000042	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1000044	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1007135	0.98[EUR][1000 genomes]
rs1007136	0.98[EUR][1000 genomes]
rs10427467	0.90[EUR][1000 genomes]
rs13044709	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13045011	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1474776	0.98[EUR][1000 genomes]
rs1535065	0.98[EUR][1000 genomes]
rs1535066	0.98[EUR][1000 genomes]
rs1569756	0.98[EUR][1000 genomes]
rs1998153	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1998154	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1998155	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs226682	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs226683	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs226684	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs226692	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs226693	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs226694	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs226695	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs226696	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs226700	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs226701	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2424647	0.97[EUR][1000 genomes]
rs2424648	0.97[EUR][1000 genomes]
rs2424651	0.92[EUR][1000 genomes]
rs2424652	0.98[EUR][1000 genomes]
rs2424653	0.88[EUR][1000 genomes]
rs2424654	0.95[EUR][1000 genomes]
rs2424655	0.98[EUR][1000 genomes]
rs2424656	0.98[EUR][1000 genomes]
rs2424657	0.98[EUR][1000 genomes]
rs2424658	0.98[EUR][1000 genomes]
rs2424659	0.98[EUR][1000 genomes]
rs2424677	0.98[EUR][1000 genomes]
rs2424679	0.97[EUR][1000 genomes]
rs2424680	0.98[EUR][1000 genomes]
rs2424682	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2424683	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2424684	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2424685	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2424686	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2892219	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4239750	0.98[EUR][1000 genomes]
rs4813531	0.98[EUR][1000 genomes]
rs4813532	0.98[EUR][1000 genomes]
rs4813534	0.98[EUR][1000 genomes]
rs4813535	0.98[EUR][1000 genomes]
rs4813536	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4813537	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4815304	0.97[EUR][1000 genomes]
rs4815305	0.98[EUR][1000 genomes]
rs4815306	0.98[EUR][1000 genomes]
rs4815309	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4815311	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6036899	0.98[EUR][1000 genomes]
rs6036900	0.98[EUR][1000 genomes]
rs6036903	0.98[EUR][1000 genomes]
rs6036905	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6036907	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6049940	0.98[EUR][1000 genomes]
rs6049941	0.98[EUR][1000 genomes]
rs6049942	0.98[EUR][1000 genomes]
rs6049944	0.98[EUR][1000 genomes]
rs6049945	0.98[EUR][1000 genomes]
rs6049947	0.98[EUR][1000 genomes]
rs6049949	0.98[EUR][1000 genomes]
rs6049950	0.98[EUR][1000 genomes]
rs6049951	0.98[EUR][1000 genomes]
rs6049963	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6049964	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6049967	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6049968	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6049970	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6076273	0.98[EUR][1000 genomes]
rs6083603	0.98[EUR][1000 genomes]
rs6083604	0.98[EUR][1000 genomes]
rs6083605	0.98[EUR][1000 genomes]
rs6083615	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083616	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083617	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083697	1.00[CHB][hapmap]
rs6106941	0.98[EUR][1000 genomes]
rs6106946	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6114860	0.98[EUR][1000 genomes]
rs6114861	0.94[EUR][1000 genomes]
rs61190607	0.98[EUR][1000 genomes]
rs6132763	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6132764	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6138371	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6138372	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62216905	0.98[EUR][1000 genomes]
rs6515532	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73101419	1.00[ASN][1000 genomes]
rs732829	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73329	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs761368	1.00[CHB][hapmap]
rs85805	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs910242	0.98[EUR][1000 genomes]
rs971956	0.96[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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2424681	C20orf3	cis	parietal	SCAN
rs2424681	C20orf191	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24744400-24751400	Weak transcription	Thymus	Thymus
2	chr20:24744600-24749000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr20:24745400-24755600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr20:24747800-24749400	Enhancers	Fetal Muscle Leg	muscle
5	chr20:24747800-24752000	Weak transcription	Primary B cells from peripheral blood	blood
6	chr20:24748200-24749200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr20:24748400-24749000	Enhancers	Fetal Thymus	thymus
8	chr20:24748400-24749200	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr20:24748400-24749800	Enhancers	HSMM	muscle
10	chr20:24748400-24749800	Enhancers	NH-A	brain
11	chr20:24748600-24749000	Enhancers	Placenta	Placenta
12	chr20:24748600-24749200	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr20:24748600-24750000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr20:24748600-24750600	Enhancers	Fetal Muscle Trunk	muscle
15	chr20:24748800-24749200	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr20:24748800-24749200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr20:24748800-24749200	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr20:24748800-24749200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr20:24748800-24749400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr20:24748800-24749600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr20:24748800-24749800	Enhancers	Placenta Amnion	Placenta Amnion
22	chr20:24748800-24750400	Enhancers	HSMMtube	muscle

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