Variant report

Variant	rs965733
Chromosome Location	chr21:45435998-45435999
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:45431927..45433865-chr21:45434646..45436317,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000160218	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs1051981	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs1131999	0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs13047030	0.91[ASN][1000 genomes]
rs13047214	0.98[ASN][1000 genomes]
rs13048791	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs13050630	0.82[EUR][1000 genomes]
rs13052507	0.89[ASN][1000 genomes]
rs17004630	0.90[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.92[JPT][hapmap];0.82[MEX][hapmap]
rs1971507	0.88[ASN][1000 genomes]
rs2006694	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs2020948	0.82[EUR][1000 genomes]
rs2071152	0.80[CEU][hapmap];0.89[TSI][hapmap]
rs2071154	0.86[CEU][hapmap];0.80[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2156428	0.81[EUR][1000 genomes]
rs2187313	0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs2238704	0.80[CEU][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs2238705	0.86[EUR][1000 genomes]
rs2238706	0.88[EUR][1000 genomes]
rs2238707	0.88[EUR][1000 genomes]
rs2238708	0.81[EUR][1000 genomes]
rs2238709	0.83[EUR][1000 genomes]
rs2238710	0.82[EUR][1000 genomes]
rs2238711	0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs2238712	0.81[EUR][1000 genomes]
rs2243348	0.87[EUR][1000 genomes]
rs2245372	0.82[EUR][1000 genomes]
rs2245380	0.82[EUR][1000 genomes]
rs2245386	0.82[EUR][1000 genomes]
rs2245462	0.80[CEU][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs2245759	0.89[EUR][1000 genomes]
rs2247400	0.81[EUR][1000 genomes]
rs2255016	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2255955	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2256392	0.88[EUR][1000 genomes]
rs2256441	0.80[CEU][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs2276532	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs2277805	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2299812	0.89[EUR][1000 genomes]
rs2299813	0.89[EUR][1000 genomes]
rs2299816	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2299817	1.00[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.84[ASN][1000 genomes]
rs2299820	0.82[EUR][1000 genomes]
rs2838464	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2838467	0.82[EUR][1000 genomes]
rs2838468	0.89[EUR][1000 genomes]
rs2838469	0.87[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.85[MKK][hapmap];0.81[TSI][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838472	0.81[EUR][1000 genomes]
rs2838476	0.96[TSI][hapmap];0.88[EUR][1000 genomes]
rs2838477	0.82[EUR][1000 genomes]
rs2838478	0.84[CEU][hapmap];0.89[EUR][1000 genomes]
rs2838480	0.89[EUR][1000 genomes]
rs2838481	0.82[EUR][1000 genomes]
rs2838483	0.82[EUR][1000 genomes]
rs2838485	0.82[EUR][1000 genomes]
rs2838507	0.89[CHB][hapmap];0.85[JPT][hapmap]
rs2838508	0.96[CHD][hapmap];0.92[GIH][hapmap];0.85[JPT][hapmap]
rs2838509	0.90[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];0.85[JPT][hapmap]
rs28385580	0.98[ASN][1000 genomes]
rs2850154	0.93[JPT][hapmap]
rs35610725	0.82[EUR][1000 genomes]
rs3788097	0.80[CEU][hapmap];0.82[TSI][hapmap]
rs3788101	0.86[EUR][1000 genomes]
rs3788102	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3788104	0.90[CHB][hapmap];0.92[JPT][hapmap]
rs3788108	0.90[CHB][hapmap];0.93[JPT][hapmap]
rs4818878	0.88[EUR][1000 genomes]
rs4818886	0.90[CHB][hapmap];0.93[CHD][hapmap]
rs4819361	0.90[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs4819362	0.90[CHB][hapmap];0.92[JPT][hapmap]
rs4819375	0.90[CHB][hapmap];0.92[JPT][hapmap]
rs59675192	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62227166	0.87[ASN][1000 genomes]
rs7275722	0.96[ASN][1000 genomes]
rs7276709	0.98[ASN][1000 genomes]
rs7279727	0.82[EUR][1000 genomes]
rs7282324	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs729882	0.88[EUR][1000 genomes]
rs7676	0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap]
rs8126754	0.81[EUR][1000 genomes]
rs8129971	0.88[EUR][1000 genomes]
rs885872	0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs915878	0.87[EUR][1000 genomes]
rs9306169	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9306171	0.80[CEU][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs9306174	0.82[EUR][1000 genomes]
rs968713	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs9974165	0.89[EUR][1000 genomes]
rs9975708	0.80[CEU][hapmap];0.82[EUR][1000 genomes]
rs9981257	0.82[EUR][1000 genomes]
rs9982663	0.80[EUR][1000 genomes]
rs9985064	0.90[CHB][hapmap];0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
4	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
5	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs965733	PWP2	cis	lymphoblastoid	seeQTL

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:45432800-45436000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr21:45433200-45452600	Weak transcription	Aorta	Aorta
3	chr21:45433400-45436000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
4	chr21:45433600-45437600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr21:45433600-45438800	Enhancers	Primary B cells from peripheral blood	blood
6	chr21:45433600-45438800	Weak transcription	Lung	lung
7	chr21:45433600-45444800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr21:45433600-45444800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr21:45433800-45439000	Weak transcription	Fetal Intestine Small	intestine
10	chr21:45433800-45444800	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr21:45433800-45448000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr21:45434000-45436000	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr21:45434000-45436000	Enhancers	Primary T cells fromperipheralblood	blood
14	chr21:45434000-45436600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr21:45434000-45436600	Enhancers	Brain Hippocampus Middle	brain
16	chr21:45434000-45437600	Weak transcription	Gastric	stomach
17	chr21:45434000-45437600	Weak transcription	Right Ventricle	heart
18	chr21:45434000-45437800	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr21:45434000-45438800	Weak transcription	Fetal Muscle Leg	muscle
20	chr21:45434000-45439200	Enhancers	Liver	Liver
21	chr21:45434000-45441400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr21:45434000-45441400	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr21:45434000-45444000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr21:45434000-45444600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr21:45434000-45444800	Weak transcription	Placenta	Placenta
26	chr21:45434200-45437200	Enhancers	Muscle Satellite Cultured Cells	--
27	chr21:45434200-45437600	Enhancers	Primary B cells from cord blood	blood
28	chr21:45434200-45438600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr21:45434200-45439000	Enhancers	Primary neutrophils fromperipheralblood	blood
30	chr21:45434200-45440400	Weak transcription	Brain Angular Gyrus	brain
31	chr21:45434200-45443400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr21:45434200-45448800	Enhancers	Primary T killer memory cells from peripheral blood	blood
33	chr21:45434200-45450800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr21:45434400-45436600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr21:45434400-45437600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr21:45434400-45440600	Weak transcription	Fetal Heart	heart
37	chr21:45434400-45441000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr21:45434400-45446800	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr21:45434400-45451000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr21:45434600-45438800	Weak transcription	Fetal Muscle Trunk	muscle
41	chr21:45434600-45439200	Weak transcription	Right Atrium	heart
42	chr21:45434600-45444800	Weak transcription	Esophagus	oesophagus
43	chr21:45434800-45436000	Weak transcription	Osteobl	bone
44	chr21:45434800-45436800	Weak transcription	Brain Cingulate Gyrus	brain
45	chr21:45434800-45436800	Weak transcription	A549	lung
46	chr21:45434800-45437200	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr21:45434800-45437600	Weak transcription	Pancreas	Pancrea
48	chr21:45434800-45437600	Weak transcription	Stomach Mucosa	stomach
49	chr21:45434800-45438400	Weak transcription	Left Ventricle	heart
50	chr21:45434800-45438600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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