Variant report

Variant	rs12233349
Chromosome Location	chr21:41084884-41084885
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:40983246..40985382-chr21:41084857..41086793,2	MCF-7	breast:
2	chr21:40951212..40954090-chr21:41083007..41085637,2	MCF-7	breast:
3	chr21:41079016..41081384-chr21:41083696..41086649,2	MCF-7	breast:
4	chr21:41083546..41085771-chr21:41107459..41109604,2	MCF-7	breast:
5	chr21:40890342..40891575-chr21:41084640..41085747,7	MCF-7	breast:
6	chr21:40889947..40890880-chr21:41084564..41085517,6	MCF-7	breast:
7	chr21:41041115..41042098-chr21:41084636..41085568,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000184809	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10483058	0.95[ASN][1000 genomes]
rs11909296	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12233297	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12233347	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12626178	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];1.00[ASN][1000 genomes]
rs16998157	0.96[ASN][1000 genomes]
rs16998163	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16998166	0.82[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs2410177	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2410178	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2837128	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55707904	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55901439	0.96[ASN][1000 genomes]
rs56112847	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57092838	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57845654	0.92[ASN][1000 genomes]
rs57952155	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58037814	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58955754	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs59101778	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59297136	0.93[ASN][1000 genomes]
rs59600504	0.91[ASN][1000 genomes]
rs59639087	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59710242	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59990779	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60661700	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60728916	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62235479	0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62235484	0.89[ASN][1000 genomes]
rs62235485	0.95[ASN][1000 genomes]
rs62235486	0.95[ASN][1000 genomes]
rs62235487	0.95[ASN][1000 genomes]
rs62235490	1.00[ASN][1000 genomes]
rs62235491	1.00[ASN][1000 genomes]
rs62235496	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62235497	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62235511	0.85[ASN][1000 genomes]
rs7282484	0.96[ASN][1000 genomes]
rs73363758	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73904404	0.85[ASN][1000 genomes]
rs8127272	0.82[ASN][1000 genomes]
rs8127619	0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1061454	chr21:40757973-41265404	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1057956	chr21:40907707-41393396	Enhancers Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv544444	chr21:40907707-41393396	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv1065086	chr21:41034806-41429078	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv544445	chr21:41034806-41429078	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv834099	chr21:41076873-41206030	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:41069000-41095000	Weak transcription	Pancreas	Pancrea
2	chr21:41075800-41101800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr21:41079400-41109600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr21:41079600-41087400	Weak transcription	Fetal Intestine Small	intestine
5	chr21:41081200-41088000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr21:41081400-41087400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr21:41081400-41088000	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr21:41083200-41103000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr21:41083600-41086000	Weak transcription	Placenta	Placenta
10	chr21:41084800-41085600	Enhancers	Duodenum Mucosa	Duodenum

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