Variant report

Variant	rs2838480
Chromosome Location	chr21:45484414-45484415
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:45483486..45486444-chr21:45498121..45500781,3	K562	blood:
2	chr21:45483073..45484734-chr21:45486730..45488826,2	K562	blood:
3	chr21:45483406..45486402-chr21:45486575..45488365,2	MCF-7	breast:
4	chr21:45483073..45485151-chr21:45486951..45488826,2	K562	blood:
5	chr21:45311589..45314501-chr21:45483569..45485379,2	MCF-7	breast:
6	chr21:45483221..45485092-chr21:45485897..45487592,2	MCF-7	breast:
7	chr21:45483653..45485370-chr21:45553833..45556700,2	K562	blood:
8	chr21:45437723..45440453-chr21:45482663..45485495,2	K562	blood:
9	chr21:45473377..45479336-chr21:45481371..45487468,11	K562	blood:
10	chr21:45431167..45434118-chr21:45483747..45486139,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000160221	Chromatin interaction
ENSG00000160218	Chromatin interaction

Extended variants
information (count: 145 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:136)

rs_ID	r²[population]
rs1059813	0.82[ASN][1000 genomes]
rs10854489	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11089111	0.82[ASN][1000 genomes]
rs1131999	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11700919	0.82[ASN][1000 genomes]
rs12627239	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs13050630	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1858665	0.82[ASN][1000 genomes]
rs2020945	0.82[ASN][1000 genomes]
rs2020946	0.82[ASN][1000 genomes]
rs2020947	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2020948	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2039272	0.86[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs2051260	0.81[ASN][1000 genomes]
rs2071142	0.82[ASN][1000 genomes]
rs2071143	0.82[ASN][1000 genomes]
rs2071146	0.82[ASN][1000 genomes]
rs2071147	0.82[ASN][1000 genomes]
rs2071152	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2071154	0.81[EUR][1000 genomes]
rs2156428	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2238704	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2238705	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2238706	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2238707	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2238708	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2238709	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2238710	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2238711	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2238712	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2238713	0.82[ASN][1000 genomes]
rs2242950	0.87[ASN][1000 genomes]
rs2242953	0.82[ASN][1000 genomes]
rs2243348	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2243999	0.82[ASN][1000 genomes]
rs2245372	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2245380	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2245386	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2245462	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2245759	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2247400	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2251267	0.82[ASN][1000 genomes]
rs2255716	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2255828	0.94[ASN][1000 genomes]
rs2255922	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2256392	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2256441	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2276530	0.91[ASN][1000 genomes]
rs2277806	0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2299812	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2299813	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2299815	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2299816	0.82[EUR][1000 genomes]
rs2299818	0.99[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2299820	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2329707	0.82[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2516519	0.82[ASN][1000 genomes]
rs2516521	0.86[AFR][1000 genomes]
rs2776368	0.82[ASN][1000 genomes]
rs2838466	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2838467	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2838468	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2838471	0.91[ASN][1000 genomes]
rs2838472	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2838473	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2838474	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2838476	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2838477	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838478	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838481	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2838482	0.98[ASN][1000 genomes]
rs2838483	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2838485	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2838486	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2838488	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs2838489	0.82[ASN][1000 genomes]
rs2838490	0.82[ASN][1000 genomes]
rs2838491	0.82[ASN][1000 genomes]
rs2838492	0.82[ASN][1000 genomes]
rs2850150	0.86[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs2850155	0.82[ASN][1000 genomes]
rs2850156	0.82[ASN][1000 genomes]
rs2850157	0.82[ASN][1000 genomes]
rs2855651	0.82[ASN][1000 genomes]
rs2855652	0.82[ASN][1000 genomes]
rs28859288	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35610725	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3788097	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3788098	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3788101	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3788102	0.82[EUR][1000 genomes]
rs4818878	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4819366	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4819370	0.89[ASN][1000 genomes]
rs4819372	0.86[ASN][1000 genomes]
rs4819373	0.82[ASN][1000 genomes]
rs4819376	0.82[ASN][1000 genomes]
rs4819377	0.82[ASN][1000 genomes]
rs4819378	0.82[ASN][1000 genomes]
rs4819379	0.82[ASN][1000 genomes]
rs56384549	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59675192	0.82[EUR][1000 genomes]
rs6518345	0.81[ASN][1000 genomes]
rs7277269	0.89[ASN][1000 genomes]
rs7279727	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7280581	0.82[ASN][1000 genomes]
rs7281270	0.86[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7281768	0.98[ASN][1000 genomes]
rs7281778	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7282643	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs729882	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs756553	0.82[ASN][1000 genomes]
rs756554	0.81[ASN][1000 genomes]
rs8126754	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8126958	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8129971	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8130647	0.82[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs8132918	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs8133422	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8133610	0.89[ASN][1000 genomes]
rs915878	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9306169	0.82[EUR][1000 genomes]
rs9306171	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9306172	0.97[ASN][1000 genomes]
rs9306174	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs965733	0.89[EUR][1000 genomes]
rs968714	0.82[ASN][1000 genomes]
rs9974165	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9974315	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9975708	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9975978	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9977564	0.90[ASN][1000 genomes]
rs9978130	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9981257	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9981485	0.85[ASN][1000 genomes]
rs9982663	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	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
4	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
5	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
6	nsv1064420	chr21:45460089-45814986	Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
7	nsv544472	chr21:45460089-45814986	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
8	nsv432155	chr21:45479055-45772388	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
9	nsv913890	chr21:45482950-45603746	Genic enhancers Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2838480	PWP2	cis	Muscle Skeletal	GTEx
rs2838480	PWP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:45445400-45509400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr21:45446400-45502200	Weak transcription	Fetal Heart	heart
3	chr21:45451000-45494400	Weak transcription	Fetal Brain Male	brain
4	chr21:45463400-45485200	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr21:45463600-45485000	Strong transcription	Thymus	Thymus
6	chr21:45465200-45485200	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr21:45465800-45485000	Strong transcription	Fetal Thymus	thymus
8	chr21:45465800-45487800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr21:45468400-45502400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr21:45468800-45502600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr21:45469400-45487000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr21:45469400-45502000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr21:45471400-45487000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr21:45471800-45495400	Strong transcription	Fetal Muscle Leg	muscle
15	chr21:45471800-45502200	Strong transcription	Fetal Intestine Small	intestine
16	chr21:45472000-45494200	Weak transcription	Psoas Muscle	Psoas
17	chr21:45472000-45502600	Strong transcription	Duodenum Mucosa	Duodenum
18	chr21:45472400-45491200	Strong transcription	Fetal Intestine Large	intestine
19	chr21:45472600-45504400	Strong transcription	Fetal Stomach	stomach
20	chr21:45472800-45503800	Strong transcription	Liver	Liver
21	chr21:45473000-45485200	Weak transcription	Colon Smooth Muscle	Colon
22	chr21:45473000-45526600	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr21:45474800-45485200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr21:45475000-45493000	Strong transcription	Fetal Muscle Trunk	muscle
25	chr21:45475000-45502600	Weak transcription	Right Atrium	heart
26	chr21:45475200-45487600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr21:45475200-45494000	Weak transcription	Fetal Kidney	kidney
28	chr21:45475600-45485800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr21:45475600-45491200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr21:45476200-45487600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr21:45476400-45485000	Weak transcription	NHDF-Ad	bronchial
32	chr21:45478200-45487000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr21:45479800-45491200	Weak transcription	Small Intestine	intestine
34	chr21:45480000-45486800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr21:45480200-45485200	Weak transcription	Hela-S3	cervix
36	chr21:45481400-45484800	Strong transcription	Primary B cells from peripheral blood	blood
37	chr21:45481400-45484800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr21:45481400-45485000	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr21:45481400-45485200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr21:45481400-45485800	Strong transcription	Osteobl	bone
41	chr21:45481400-45487600	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr21:45481400-45498400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr21:45481600-45484600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr21:45481600-45484600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr21:45481600-45484800	Strong transcription	NH-A	brain
46	chr21:45481600-45485600	Strong transcription	Skeletal Muscle Male	skeletal muscle
47	chr21:45481600-45485600	Strong transcription	NHEK	skin
48	chr21:45481600-45486000	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr21:45481600-45486600	Strong transcription	HUES48 Cell Line	embryonic stem cell
50	chr21:45481600-45487600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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