Variant report

Variant	rs2330247
Chromosome Location	chr21:47262390-47262391
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	chr21:47261675..47263685-chr21:47264908..47267325,2	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11700891	0.93[ASN][1000 genomes]
rs11908836	1.00[JPT][hapmap]
rs11911348	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs12106367	0.83[ASN][1000 genomes]
rs1810871	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2015400	0.94[CEU][hapmap];0.83[CHB][hapmap]
rs2277814	0.91[CHB][hapmap]
rs2330328	0.94[CEU][hapmap];1.00[CHB][hapmap]
rs2838977	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs2839008	0.81[CEU][hapmap];0.80[TSI][hapmap]
rs2839022	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2839023	0.94[CEU][hapmap];1.00[CHB][hapmap]
rs2839024	0.94[CEU][hapmap];1.00[CHB][hapmap]
rs2839025	0.83[CHB][hapmap]
rs2839078	0.91[CHB][hapmap]
rs2877094	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34530304	0.88[ASN][1000 genomes]
rs4818806	0.88[ASN][1000 genomes]
rs4818807	0.88[ASN][1000 genomes]
rs4819142	0.81[CHB][hapmap]
rs4819153	1.00[ASN][1000 genomes]
rs4819160	0.87[CEU][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs725930	0.81[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs7278258	0.91[CHB][hapmap]
rs7279037	1.00[ASN][1000 genomes]
rs7280089	0.81[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs73382517	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs741954	0.94[CEU][hapmap];0.91[CHB][hapmap]
rs8127512	0.88[ASN][1000 genomes]
rs8133338	0.81[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap]
rs9977276	0.91[CHB][hapmap]
rs9977594	0.81[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs9983643	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9983803	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9984438	0.94[CEU][hapmap];0.90[CHB][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531546	chr21:46504151-47411772	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
2	nsv1058665	chr21:46719445-47634282	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	91 gene(s)	inside rSNPs	diseases
3	nsv544486	chr21:46719445-47634282	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	91 gene(s)	inside rSNPs	diseases
4	nsv1059230	chr21:46956877-47907990	Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	n/a
5	nsv544491	chr21:46956877-47907990	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	n/a
6	nsv1058472	chr21:47027823-47797326	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	n/a
7	nsv544492	chr21:47027823-47797326	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	n/a
8	nsv428043	chr21:47179244-47471971	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	n/a
9	nsv1065959	chr21:47188878-48091343	Bivalent Enhancer Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	n/a
10	nsv914078	chr21:47218744-47311686	Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
11	nsv531580	chr21:47221774-48090317	Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	n/a
12	esv2756755	chr21:47243032-47319768	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
13	esv2758821	chr21:47243032-47319768	Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
14	nsv914079	chr21:47243074-47650362	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2330247	PCBP3	cis	cerebellum	SCAN
rs2330247	KRTAP10-5	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47261200-47264600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr21:47261200-47265200	Weak transcription	Fetal Brain Male	brain
3	chr21:47261200-47266400	Weak transcription	Fetal Kidney	kidney
4	chr21:47261200-47267800	Weak transcription	NH-A	brain
5	chr21:47261200-47269600	Weak transcription	Thymus	Thymus
6	chr21:47261800-47275200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr21:47262000-47262400	Enhancers	HSMMtube	muscle
8	chr21:47262000-47263000	Weak transcription	HSMM	muscle
9	chr21:47262000-47265400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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