Variant report

Variant	rs2299813
Chromosome Location	chr21:45439053-45439054
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:45437723..45440453-chr21:45482663..45485495,2	K562	blood:
2	chr21:45361403..45363347-chr21:45436825..45439305,2	K562	blood:
3	chr21:45438119..45440694-chr21:45475384..45477960,3	K562	blood:
4	chr21:45361847..45364685-chr21:45436825..45439426,2	K562	blood:
5	chr21:45438832..45440395-chr21:45529682..45531391,2	K562	blood:
6	chr21:45430739..45433866-chr21:45436879..45444885,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000160218	Chromatin interaction

Extended variants
information (count: 101 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10854489	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1131999	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12627239	0.82[ASN][1000 genomes]
rs13050630	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2020947	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2020948	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2039272	0.82[ASN][1000 genomes]
rs2071152	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2071154	0.81[EUR][1000 genomes]
rs2156428	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2238704	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2238705	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2238706	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2238707	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2238708	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2238709	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2238710	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2238711	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2238712	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2242950	0.82[ASN][1000 genomes]
rs2243348	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2245372	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2245380	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2245386	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2245462	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2245759	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2247400	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2255716	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2255828	0.86[ASN][1000 genomes]
rs2255922	0.88[ASN][1000 genomes]
rs2256392	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2256441	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2276530	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2277806	0.85[ASN][1000 genomes]
rs2299812	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2299815	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2299816	0.82[EUR][1000 genomes]
rs2299818	0.89[ASN][1000 genomes]
rs2299820	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2838466	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2838467	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2838468	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2838471	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2838472	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838473	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2838474	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2838476	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2838477	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2838478	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2838480	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2838481	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2838482	0.89[ASN][1000 genomes]
rs2838483	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2838485	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2838486	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2838488	0.82[ASN][1000 genomes]
rs2850150	0.82[ASN][1000 genomes]
rs28859288	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35610725	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3788097	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3788098	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3788101	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3788102	0.82[EUR][1000 genomes]
rs4818878	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4819366	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4819370	0.83[ASN][1000 genomes]
rs4819372	0.81[ASN][1000 genomes]
rs56384549	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59675192	0.82[EUR][1000 genomes]
rs7277269	0.83[ASN][1000 genomes]
rs7279727	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7281270	0.82[ASN][1000 genomes]
rs7281768	0.89[ASN][1000 genomes]
rs7281778	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7282643	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs729882	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8126754	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8126958	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8129971	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8132918	0.83[ASN][1000 genomes]
rs8133422	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8133610	0.83[ASN][1000 genomes]
rs915878	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9306169	0.82[EUR][1000 genomes]
rs9306171	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9306172	0.94[ASN][1000 genomes]
rs9306174	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs965733	0.89[EUR][1000 genomes]
rs9974165	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9974315	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9975708	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9975978	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9977564	0.85[ASN][1000 genomes]
rs9978130	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9981257	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9982663	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2299813	PWP2	cis	Muscle Skeletal	GTEx
rs2299813	PWP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:45433200-45452600	Weak transcription	Aorta	Aorta
2	chr21:45433600-45444800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr21:45433600-45444800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr21:45433800-45444800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr21:45433800-45448000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr21:45434000-45439200	Enhancers	Liver	Liver
7	chr21:45434000-45441400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr21:45434000-45441400	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr21:45434000-45444000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr21:45434000-45444600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr21:45434000-45444800	Weak transcription	Placenta	Placenta
12	chr21:45434200-45440400	Weak transcription	Brain Angular Gyrus	brain
13	chr21:45434200-45443400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr21:45434200-45448800	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr21:45434200-45450800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr21:45434400-45440600	Weak transcription	Fetal Heart	heart
17	chr21:45434400-45441000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr21:45434400-45446800	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr21:45434400-45451000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr21:45434600-45439200	Weak transcription	Right Atrium	heart
21	chr21:45434600-45444800	Weak transcription	Esophagus	oesophagus
22	chr21:45434800-45440200	Enhancers	Dnd41	blood
23	chr21:45434800-45440400	Weak transcription	Stomach Smooth Muscle	stomach
24	chr21:45434800-45440600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr21:45434800-45440600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr21:45434800-45440600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr21:45434800-45441400	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr21:45434800-45444800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr21:45434800-45444800	Weak transcription	Fetal Intestine Large	intestine
30	chr21:45434800-45444800	Weak transcription	HSMM	muscle
31	chr21:45434800-45445000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr21:45434800-45447200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr21:45434800-45447400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr21:45435000-45440000	Enhancers	Primary hematopoietic stem cells	blood
35	chr21:45435000-45440000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr21:45435000-45440400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr21:45435000-45440600	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr21:45435000-45441000	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr21:45435000-45444000	Weak transcription	NHEK	skin
40	chr21:45435000-45444600	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr21:45435000-45444800	Enhancers	Primary T helper cells PMA-I stimulated	--
42	chr21:45435000-45450200	Enhancers	Primary T helper naive cells from peripheral blood	blood
43	chr21:45435200-45445200	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr21:45435400-45444200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr21:45435800-45444200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr21:45436000-45442200	Enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr21:45436400-45444200	Weak transcription	Osteobl	bone
48	chr21:45436400-45444800	Weak transcription	HMEC	breast
49	chr21:45436600-45444800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr21:45436800-45446800	Enhancers	Primary T cells fromperipheralblood	blood

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