Variant report

Variant	rs8126754
Chromosome Location	chr21:45450869-45450870
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:45431046..45433017-chr21:45448957..45451202,3	MCF-7	breast:
2	chr21:45449259..45451430-chr21:45484484..45487019,2	K562	blood:
3	chr21:45449660..45451508-chr21:45454288..45457087,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000160218	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10854489	1.00[ASN][1000 genomes]
rs1131999	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12627239	0.82[ASN][1000 genomes]
rs13050630	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2020947	1.00[ASN][1000 genomes]
rs2020948	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2039272	0.82[ASN][1000 genomes]
rs2071152	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2071154	0.85[EUR][1000 genomes]
rs2156428	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2238704	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2238705	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2238706	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2238707	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2238708	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2238709	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2238710	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2238711	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2238712	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2242950	0.82[ASN][1000 genomes]
rs2243348	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2245372	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2245380	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2245386	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2245462	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2245759	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2247400	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2255716	0.89[ASN][1000 genomes]
rs2255828	0.86[ASN][1000 genomes]
rs2255922	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2256392	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2256441	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2276530	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2277806	0.85[ASN][1000 genomes]
rs2299812	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2299813	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2299815	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2299816	0.87[EUR][1000 genomes]
rs2299818	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2299820	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2838466	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2838467	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2838468	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2838471	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838472	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838473	0.97[ASN][1000 genomes]
rs2838474	0.94[ASN][1000 genomes]
rs2838476	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2838477	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2838478	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2838480	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2838481	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2838482	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2838483	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2838485	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2838486	0.86[ASN][1000 genomes]
rs2838488	0.82[ASN][1000 genomes]
rs2850150	0.82[ASN][1000 genomes]
rs28859288	0.91[ASN][1000 genomes]
rs35610725	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3788097	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3788098	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3788101	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3788102	0.87[EUR][1000 genomes]
rs4818878	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4819366	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4819370	0.83[ASN][1000 genomes]
rs4819372	0.81[ASN][1000 genomes]
rs56384549	0.93[ASN][1000 genomes]
rs59675192	0.87[EUR][1000 genomes]
rs7277269	0.83[ASN][1000 genomes]
rs7279727	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7281270	0.82[ASN][1000 genomes]
rs7281768	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7281778	0.97[ASN][1000 genomes]
rs7282643	1.00[ASN][1000 genomes]
rs729882	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8126958	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8129971	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8132918	0.83[ASN][1000 genomes]
rs8133422	0.94[ASN][1000 genomes]
rs8133610	0.83[ASN][1000 genomes]
rs915878	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9306169	0.87[EUR][1000 genomes]
rs9306171	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9306172	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9306174	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs965733	0.81[EUR][1000 genomes]
rs9974165	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9974315	0.94[ASN][1000 genomes]
rs9975708	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9975978	0.89[ASN][1000 genomes]
rs9977564	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9978130	0.97[ASN][1000 genomes]
rs9981257	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9982663	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[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	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
6	nsv1064549	chr21:45446358-45493720	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs8126754	PWP2	cis	Muscle Skeletal	GTEx
rs8126754	PWP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:45433200-45452600	Weak transcription	Aorta	Aorta
2	chr21:45434400-45451000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr21:45438200-45451400	Weak transcription	Hela-S3	cervix
4	chr21:45440800-45451400	Weak transcription	Dnd41	blood
5	chr21:45441800-45452400	Weak transcription	Fetal Brain Female	brain
6	chr21:45444400-45452400	Weak transcription	Fetal Intestine Small	intestine
7	chr21:45445200-45452400	Weak transcription	Esophagus	oesophagus
8	chr21:45445200-45454400	Weak transcription	A549	lung
9	chr21:45445200-45454600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr21:45445200-45457800	Weak transcription	Small Intestine	intestine
11	chr21:45445200-45471400	Weak transcription	Stomach Mucosa	stomach
12	chr21:45445400-45454400	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr21:45445400-45454600	Weak transcription	Colonic Mucosa	Colon
14	chr21:45445400-45509400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr21:45445600-45452600	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr21:45445800-45451200	Weak transcription	Pancreas	Pancrea
17	chr21:45445800-45452800	Weak transcription	Fetal Lung	lung
18	chr21:45445800-45457800	Weak transcription	Gastric	stomach
19	chr21:45445800-45458200	Weak transcription	HSMMtube	muscle
20	chr21:45445800-45471400	Weak transcription	Right Atrium	heart
21	chr21:45446000-45451400	Weak transcription	Fetal Intestine Large	intestine
22	chr21:45446000-45452400	Weak transcription	Fetal Muscle Leg	muscle
23	chr21:45446000-45452600	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr21:45446000-45452600	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr21:45446000-45452600	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr21:45446000-45452600	Weak transcription	HSMM	muscle
27	chr21:45446000-45452600	Weak transcription	HUVEC	blood vessel
28	chr21:45446200-45451400	Weak transcription	Liver	Liver
29	chr21:45446200-45452200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr21:45446200-45452400	Weak transcription	Duodenum Mucosa	Duodenum
31	chr21:45446200-45452400	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr21:45446200-45452400	Weak transcription	HMEC	breast
33	chr21:45446200-45452600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr21:45446200-45452600	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr21:45446200-45452800	Weak transcription	Stomach Smooth Muscle	stomach
36	chr21:45446200-45453000	Weak transcription	Rectal Smooth Muscle	rectum
37	chr21:45446200-45453800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr21:45446200-45454200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr21:45446200-45454400	Weak transcription	Colon Smooth Muscle	Colon
40	chr21:45446200-45454600	Weak transcription	NHLF	lung
41	chr21:45446400-45451400	Weak transcription	Primary T cells from cord blood	blood
42	chr21:45446400-45452000	Weak transcription	NHDF-Ad	bronchial
43	chr21:45446400-45452000	Weak transcription	Osteobl	bone
44	chr21:45446400-45452200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr21:45446400-45452200	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr21:45446400-45452400	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr21:45446400-45452600	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr21:45446400-45452600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr21:45446400-45452600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr21:45446400-45453400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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