Variant report

Variant	rs2838466
Chromosome Location	chr21:45435187-45435188
allele	A/T
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: 158 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:153)

rs_ID	r²[population]
rs1059813	0.85[EUR][1000 genomes]
rs10854489	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11089111	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11089115	0.81[EUR][1000 genomes]
rs1131999	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11700919	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12627239	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13046297	0.81[EUR][1000 genomes]
rs13047030	0.84[EUR][1000 genomes]
rs13050630	0.88[ASN][1000 genomes]
rs1858665	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2020945	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2020946	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2020947	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2020948	0.89[ASN][1000 genomes]
rs2039272	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2051260	0.83[EUR][1000 genomes]
rs2071142	0.84[EUR][1000 genomes]
rs2071143	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2071146	0.85[EUR][1000 genomes]
rs2071147	0.85[EUR][1000 genomes]
rs2071152	0.85[ASN][1000 genomes]
rs2073432	0.82[EUR][1000 genomes]
rs2073433	0.85[EUR][1000 genomes]
rs2073435	0.84[EUR][1000 genomes]
rs2156428	0.88[ASN][1000 genomes]
rs2238704	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2238705	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2238706	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2238707	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2238708	0.98[ASN][1000 genomes]
rs2238709	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2238710	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2238711	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2238712	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2238713	0.84[EUR][1000 genomes]
rs2242950	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2242953	0.84[EUR][1000 genomes]
rs2242954	0.80[EUR][1000 genomes]
rs2243348	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2243999	0.86[EUR][1000 genomes]
rs2245372	0.86[ASN][1000 genomes]
rs2245380	0.88[ASN][1000 genomes]
rs2245386	0.86[ASN][1000 genomes]
rs2245462	0.86[ASN][1000 genomes]
rs2245759	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2247400	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2251267	0.85[EUR][1000 genomes]
rs2255716	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2255828	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2255922	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2255955	0.90[EUR][1000 genomes]
rs2256392	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2256441	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2276530	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2277805	0.83[EUR][1000 genomes]
rs2277806	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2299812	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2299813	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2299815	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2299818	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2299820	0.86[ASN][1000 genomes]
rs2329707	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2516519	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2516521	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2776368	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2838467	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2838468	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838469	0.90[EUR][1000 genomes]
rs2838471	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2838472	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2838473	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2838474	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2838476	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2838477	0.89[ASN][1000 genomes]
rs2838478	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2838480	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2838481	0.88[ASN][1000 genomes]
rs2838482	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2838483	0.88[ASN][1000 genomes]
rs2838485	0.86[ASN][1000 genomes]
rs2838486	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2838488	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2838489	0.85[EUR][1000 genomes]
rs2838490	0.84[EUR][1000 genomes]
rs2838491	0.85[EUR][1000 genomes]
rs2838492	0.85[EUR][1000 genomes]
rs2838494	0.84[EUR][1000 genomes]
rs2838496	0.83[EUR][1000 genomes]
rs2838498	0.84[EUR][1000 genomes]
rs2838499	0.83[EUR][1000 genomes]
rs2850150	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2850155	0.86[EUR][1000 genomes]
rs2850156	0.84[EUR][1000 genomes]
rs2850157	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2855651	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2855652	0.84[EUR][1000 genomes]
rs28859288	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35538274	0.83[EUR][1000 genomes]
rs35610725	0.88[ASN][1000 genomes]
rs3788097	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3788098	1.00[ASN][1000 genomes]
rs3788101	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4818878	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4818881	0.83[EUR][1000 genomes]
rs4818882	0.81[EUR][1000 genomes]
rs4819366	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4819370	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4819372	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4819373	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4819376	0.84[EUR][1000 genomes]
rs4819377	0.85[EUR][1000 genomes]
rs4819378	0.84[EUR][1000 genomes]
rs4819379	0.83[EUR][1000 genomes]
rs4819381	0.84[EUR][1000 genomes]
rs56384549	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62229738	0.82[EUR][1000 genomes]
rs7277269	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7279727	0.97[ASN][1000 genomes]
rs7280581	0.85[EUR][1000 genomes]
rs7281270	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7281768	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7281778	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7282643	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7283870	0.81[EUR][1000 genomes]
rs729882	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs756553	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs756554	0.81[EUR][1000 genomes]
rs756555	0.83[EUR][1000 genomes]
rs8126564	0.84[EUR][1000 genomes]
rs8126754	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs8126958	0.93[ASN][1000 genomes]
rs8129971	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8130647	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8132918	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8133422	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8133610	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs915878	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9306171	0.98[ASN][1000 genomes]
rs9306172	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9306174	0.86[ASN][1000 genomes]
rs9680179	0.82[EUR][1000 genomes]
rs968714	0.85[EUR][1000 genomes]
rs9974165	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9974315	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9975708	0.86[ASN][1000 genomes]
rs9975978	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9977564	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9978130	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9979882	0.81[EUR][1000 genomes]
rs9981257	0.85[ASN][1000 genomes]
rs9981485	0.85[EUR][1000 genomes]
rs9982663	0.90[AFR][1000 genomes];0.96[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2838466	PWP2	Cis_1M	lymphoblastoid	RTeQTL

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	chr21:45433200-45435200	Flanking Active TSS	K562	blood
3	chr21:45433200-45452600	Weak transcription	Aorta	Aorta
4	chr21:45433400-45436000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
5	chr21:45433600-45437600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr21:45433600-45438800	Enhancers	Primary B cells from peripheral blood	blood
7	chr21:45433600-45438800	Weak transcription	Lung	lung
8	chr21:45433600-45444800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr21:45433600-45444800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr21:45433800-45435200	Enhancers	Pancreatic Islets	Pancreatic Islet
11	chr21:45433800-45439000	Weak transcription	Fetal Intestine Small	intestine
12	chr21:45433800-45444800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr21:45433800-45448000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr21:45434000-45435200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr21:45434000-45435400	Weak transcription	Psoas Muscle	Psoas
16	chr21:45434000-45435600	Enhancers	Fetal Thymus	thymus
17	chr21:45434000-45436000	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr21:45434000-45436000	Enhancers	Primary T cells fromperipheralblood	blood
19	chr21:45434000-45436600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr21:45434000-45436600	Enhancers	Brain Hippocampus Middle	brain
21	chr21:45434000-45437600	Weak transcription	Gastric	stomach
22	chr21:45434000-45437600	Weak transcription	Right Ventricle	heart
23	chr21:45434000-45437800	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr21:45434000-45438800	Weak transcription	Fetal Muscle Leg	muscle
25	chr21:45434000-45439200	Enhancers	Liver	Liver
26	chr21:45434000-45441400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr21:45434000-45441400	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr21:45434000-45444000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr21:45434000-45444600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr21:45434000-45444800	Weak transcription	Placenta	Placenta
31	chr21:45434200-45435200	Enhancers	HepG2	liver
32	chr21:45434200-45435200	Enhancers	HMEC	breast
33	chr21:45434200-45435400	Enhancers	Duodenum Mucosa	Duodenum
34	chr21:45434200-45435800	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr21:45434200-45437200	Enhancers	Muscle Satellite Cultured Cells	--
36	chr21:45434200-45437600	Enhancers	Primary B cells from cord blood	blood
37	chr21:45434200-45438600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr21:45434200-45439000	Enhancers	Primary neutrophils fromperipheralblood	blood
39	chr21:45434200-45440400	Weak transcription	Brain Angular Gyrus	brain
40	chr21:45434200-45443400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr21:45434200-45448800	Enhancers	Primary T killer memory cells from peripheral blood	blood
42	chr21:45434200-45450800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
43	chr21:45434400-45435400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr21:45434400-45436600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr21:45434400-45437600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr21:45434400-45440600	Weak transcription	Fetal Heart	heart
47	chr21:45434400-45441000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr21:45434400-45446800	Enhancers	Primary T helper cells fromperipheralblood	blood
49	chr21:45434400-45451000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
50	chr21:45434600-45438800	Weak transcription	Fetal Muscle Trunk	muscle

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