Variant report

Variant	rs13049059
Chromosome Location	chr21:45421650-45421651
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:45418408..45422814-chr21:45429563..45432398,4	MCF-7	breast:
2	chr21:45418903..45427442-chr21:45428252..45434057,14	K562	blood:
3	chr21:45418511..45420915-chr21:45421558..45424154,3	K562	blood:
4	chr21:45419220..45421707-chr21:45432481..45434970,2	MCF-7	breast:
5	chr21:45409643..45411374-chr21:45420843..45423810,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000160218	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs1005046	0.89[JPT][hapmap]
rs11089115	0.94[JPT][hapmap]
rs1131999	0.95[GIH][hapmap];1.00[JPT][hapmap]
rs12627239	1.00[JPT][hapmap]
rs13046297	0.81[JPT][hapmap]
rs1858665	1.00[JPT][hapmap]
rs1972272	0.99[ASN][1000 genomes]
rs2020945	0.93[GIH][hapmap];1.00[JPT][hapmap]
rs2020946	1.00[JPT][hapmap]
rs2020948	1.00[JPT][hapmap]
rs2071142	0.93[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap]
rs2071143	0.93[GIH][hapmap];1.00[JPT][hapmap]
rs2071146	1.00[JPT][hapmap]
rs2071152	0.95[GIH][hapmap];1.00[JPT][hapmap]
rs2073432	1.00[JPT][hapmap]
rs2073433	0.95[JPT][hapmap]
rs2156428	1.00[JPT][hapmap]
rs2238704	0.95[GIH][hapmap];1.00[JPT][hapmap]
rs2238707	1.00[JPT][hapmap]
rs2238711	0.95[GIH][hapmap];1.00[JPT][hapmap]
rs2242950	1.00[JPT][hapmap]
rs2242953	1.00[JPT][hapmap]
rs2242954	1.00[JPT][hapmap]
rs2243999	0.93[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap]
rs2245380	1.00[JPT][hapmap]
rs2245386	1.00[JPT][hapmap]
rs2245462	0.95[GIH][hapmap];1.00[JPT][hapmap]
rs2245759	1.00[JPT][hapmap]
rs2247400	0.95[JPT][hapmap]
rs2251267	0.93[GIH][hapmap];1.00[JPT][hapmap]
rs2255716	1.00[JPT][hapmap]
rs2255828	0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap]
rs2256441	0.95[GIH][hapmap];1.00[JPT][hapmap]
rs2276530	1.00[JPT][hapmap]
rs2277806	0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs2299812	1.00[JPT][hapmap]
rs2299815	1.00[JPT][hapmap]
rs2299820	1.00[JPT][hapmap]
rs2516519	1.00[JPT][hapmap]
rs2516521	0.90[JPT][hapmap]
rs2838464	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2838468	1.00[JPT][hapmap]
rs2838469	0.81[TSI][hapmap]
rs2838472	0.95[GIH][hapmap];0.85[JPT][hapmap]
rs2838473	1.00[JPT][hapmap]
rs2838476	0.95[GIH][hapmap];1.00[JPT][hapmap]
rs2838477	1.00[JPT][hapmap]
rs2838478	1.00[JPT][hapmap]
rs2838482	1.00[JPT][hapmap]
rs2838483	1.00[JPT][hapmap]
rs2838485	1.00[JPT][hapmap]
rs2838486	0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap]
rs2838488	1.00[JPT][hapmap]
rs2838489	1.00[JPT][hapmap]
rs2838490	0.93[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap]
rs2838491	0.93[GIH][hapmap];1.00[JPT][hapmap]
rs2838492	1.00[JPT][hapmap]
rs2838494	1.00[JPT][hapmap]
rs2838496	0.95[JPT][hapmap]
rs2838502	0.93[GIH][hapmap];0.90[JPT][hapmap];0.80[TSI][hapmap]
rs2838503	0.91[GIH][hapmap];0.95[JPT][hapmap]
rs2838508	0.82[TSI][hapmap]
rs3788097	0.95[GIH][hapmap];1.00[JPT][hapmap]
rs4818881	0.89[JPT][hapmap]
rs4819362	0.94[CEU][hapmap];0.96[EUR][1000 genomes]
rs4819366	1.00[JPT][hapmap]
rs4819376	0.93[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap]
rs4819378	1.00[JPT][hapmap]
rs62229738	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6518345	0.85[JPT][hapmap]
rs7277269	0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs7279727	1.00[JPT][hapmap]
rs7280558	0.93[GIH][hapmap];0.89[JPT][hapmap]
rs7281768	1.00[JPT][hapmap]
rs729882	0.95[JPT][hapmap]
rs756554	0.93[GIH][hapmap];1.00[JPT][hapmap]
rs8126564	0.95[JPT][hapmap]
rs8126958	0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.81[ASN][1000 genomes]
rs915772	0.84[JPT][hapmap]
rs915774	0.95[GIH][hapmap]
rs915878	1.00[JPT][hapmap]
rs9306171	0.91[GIH][hapmap];1.00[JPT][hapmap]
rs9306172	0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs968714	0.93[GIH][hapmap];1.00[JPT][hapmap]
rs9975708	1.00[JPT][hapmap]
rs9981257	1.00[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	esv33817	chr21:45169412-46031810	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
2	nsv913887	chr21:45344799-45670770	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv913888	chr21:45351206-45428278	Genic enhancers Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv1063752	chr21:45406095-45460342	Flanking Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv459293	chr21:45415913-45555079	Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	nsv587721	chr21:45415913-45555079	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs13049059	PWP2	cis	lymphoblastoid	seeQTL
rs13049059	C21orf33	cis	parietal	SCAN
rs13049059	TRAPPC10	cis	cerebellum	SCAN
rs13049059	PWP2	cis	parietal	SCAN
rs13049059	C21orf129	cis	cerebellum	SCAN
rs13049059	ABCG1	cis	cerebellum	SCAN
rs13049059	ABCG1	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:45418200-45421800	Enhancers	Brain Hippocampus Middle	brain
2	chr21:45419000-45421800	Enhancers	Brain Inferior Temporal Lobe	brain
3	chr21:45420600-45425400	Weak transcription	HSMM	muscle
4	chr21:45420800-45425200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr21:45421000-45422000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr21:45421000-45425400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr21:45421000-45425600	Weak transcription	HSMMtube	muscle
8	chr21:45421400-45430400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr21:45421400-45430600	Weak transcription	Brain Cingulate Gyrus	brain
10	chr21:45421600-45431000	Weak transcription	Brain Angular Gyrus	brain
11	chr21:45421600-45431000	Weak transcription	Brain Substantia Nigra	brain

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