Variant report

Variant	rs8126958
Chromosome Location	chr21:45428278-45428279
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	chr21:45371704..45374337-chr21:45426756..45428493,2	K562	blood:
2	chr21:45424075..45428329-chr21:45429295..45434139,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000160218	Chromatin interaction

Extended variants
information (count: 125 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs1005046	0.88[CHB][hapmap];0.89[JPT][hapmap]
rs10854489	0.89[YRI][hapmap];0.96[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs11089115	0.88[CHB][hapmap];0.94[JPT][hapmap]
rs1131999	0.87[CEU][hapmap];0.81[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.86[EUR][1000 genomes]
rs12627239	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs13046297	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs13049059	0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.81[ASN][1000 genomes]
rs13050630	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1858665	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs2020945	0.88[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap]
rs2020946	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs2020947	0.94[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2020948	0.94[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2071142	0.88[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap]
rs2071143	0.82[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap]
rs2071146	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs2071152	0.94[CEU][hapmap];0.88[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.82[EUR][1000 genomes]
rs2071154	0.87[CEU][hapmap]
rs2073432	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs2073433	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs2156428	0.93[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2238704	0.88[ASW][hapmap];0.94[CEU][hapmap];0.88[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2238705	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2238706	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2238707	0.94[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2238708	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2238709	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2238710	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2238711	0.88[ASW][hapmap];0.94[CEU][hapmap];0.88[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2238712	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2242950	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs2242953	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs2242954	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs2243348	0.88[EUR][1000 genomes]
rs2243999	0.88[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap]
rs2245372	0.84[EUR][1000 genomes]
rs2245380	0.94[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2245386	0.94[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs2245462	0.94[CEU][hapmap];0.88[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.83[EUR][1000 genomes]
rs2245759	0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs2247400	0.94[CEU][hapmap];0.88[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2251267	0.88[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap]
rs2255716	0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2255828	0.88[CHB][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap]
rs2256392	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2256441	0.88[ASW][hapmap];0.94[CEU][hapmap];0.88[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2276530	0.88[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2277806	0.88[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap]
rs2299812	0.94[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2299813	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2299815	0.88[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2299816	0.81[CEU][hapmap]
rs2299818	0.81[ASN][1000 genomes]
rs2299820	0.94[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs2516519	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs2516521	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs2838466	0.93[ASN][1000 genomes]
rs2838467	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2838468	0.94[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2838471	0.91[ASN][1000 genomes]
rs2838472	0.88[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2838473	0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2838474	0.85[ASN][1000 genomes]
rs2838476	0.94[CEU][hapmap];0.88[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2838477	0.94[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2838478	0.93[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2838480	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2838481	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2838482	0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2838483	0.94[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2838485	0.94[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs2838486	0.88[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap]
rs2838488	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs2838489	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs2838490	0.88[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap]
rs2838491	0.88[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap]
rs2838492	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs2838494	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs2838496	0.88[CHB][hapmap];0.95[JPT][hapmap]
rs2838502	0.88[CHB][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap]
rs2838503	0.88[CHB][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap]
rs28859288	0.82[ASN][1000 genomes]
rs35610725	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3788097	0.82[ASW][hapmap];0.94[CEU][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3788098	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3788101	0.89[EUR][1000 genomes]
rs4818878	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4818881	0.88[CHB][hapmap];0.89[JPT][hapmap]
rs4819366	0.94[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4819376	0.88[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap]
rs4819378	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs56384549	0.85[ASN][1000 genomes]
rs6518345	0.84[CHB][hapmap];0.85[JPT][hapmap]
rs7277269	0.88[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap]
rs7279727	0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7280558	0.88[CHB][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap]
rs7281768	0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7281778	0.89[ASN][1000 genomes]
rs7282643	0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs729882	0.94[CEU][hapmap];0.88[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs756554	0.88[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap]
rs8126564	0.88[CHB][hapmap];0.95[JPT][hapmap]
rs8126754	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8129971	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8133422	0.85[ASN][1000 genomes]
rs915772	0.88[CHB][hapmap];0.84[JPT][hapmap]
rs915774	0.95[GIH][hapmap]
rs915878	0.94[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs9306171	0.94[ASW][hapmap];0.94[CEU][hapmap];0.88[CHB][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.85[MEX][hapmap];0.92[MKK][hapmap];0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9306172	0.88[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9306174	0.84[EUR][1000 genomes]
rs968714	0.88[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap]
rs9974165	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9974315	0.85[ASN][1000 genomes]
rs9975708	0.94[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs9975978	0.81[ASN][1000 genomes]
rs9978130	0.89[ASN][1000 genomes]
rs9981257	0.94[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs9982663	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs8126958	PWP2	cis	lymphoblastoid	seeQTL
rs8126958	PWP2	cis	Muscle Skeletal	GTEx
rs8126958	PWP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:45421400-45430400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr21:45421400-45430600	Weak transcription	Brain Cingulate Gyrus	brain
3	chr21:45421600-45431000	Weak transcription	Brain Angular Gyrus	brain
4	chr21:45421600-45431000	Weak transcription	Brain Substantia Nigra	brain
5	chr21:45421800-45430200	Weak transcription	Brain Hippocampus Middle	brain
6	chr21:45423400-45431000	Weak transcription	Thymus	Thymus
7	chr21:45425600-45428400	Enhancers	NH-A	brain
8	chr21:45426400-45430400	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr21:45426400-45431000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr21:45426400-45431000	Weak transcription	Liver	Liver
11	chr21:45426400-45431000	Weak transcription	Colon Smooth Muscle	Colon
12	chr21:45426400-45431200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr21:45426400-45431600	Weak transcription	Lung	lung
14	chr21:45426600-45429800	Weak transcription	HepG2	liver
15	chr21:45426800-45430600	Weak transcription	Adipose Nuclei	Adipose
16	chr21:45426800-45430600	Weak transcription	Placenta	Placenta
17	chr21:45426800-45431000	Weak transcription	A549	lung
18	chr21:45427000-45428400	Enhancers	Muscle Satellite Cultured Cells	--
19	chr21:45427000-45428600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr21:45427000-45429800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr21:45427000-45430000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr21:45427000-45430000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr21:45427000-45430400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr21:45427000-45430800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr21:45427000-45430800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr21:45427000-45430800	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr21:45427000-45430800	Weak transcription	HUVEC	blood vessel
28	chr21:45427000-45431000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr21:45427000-45431000	Weak transcription	Stomach Smooth Muscle	stomach
30	chr21:45427000-45431000	Weak transcription	Hela-S3	cervix
31	chr21:45427000-45431000	Weak transcription	NHEK	skin
32	chr21:45427000-45431000	Weak transcription	NHLF	lung
33	chr21:45427000-45431200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr21:45427000-45431200	Weak transcription	HMEC	breast
35	chr21:45427400-45430600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr21:45427400-45431000	Weak transcription	Fetal Intestine Small	intestine
37	chr21:45427600-45431200	Weak transcription	NHDF-Ad	bronchial
38	chr21:45427800-45430000	Weak transcription	HSMM	muscle
39	chr21:45427800-45430400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr21:45427800-45430400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr21:45427800-45430600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr21:45427800-45430800	Weak transcription	Osteobl	bone
43	chr21:45427800-45431200	Weak transcription	HSMMtube	muscle
44	chr21:45428000-45430200	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr21:45428200-45429200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr21:45428200-45430600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr21:45428200-45431000	Weak transcription	Fetal Thymus	thymus

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