Variant report

Variant	rs2183573
Chromosome Location	chr21:40574305-40574306
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F4	chr21:40574278-40574478	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr21:40572950-40574437	K562	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:40574233..40577132-chr21:40589410..40591916,2	MCF-7	breast:
2	chr21:40551398..40560769-chr21:40565658..40576445,18	K562	blood:
3	chr21:40572513..40574905-chr21:40578164..40579984,2	MCF-7	breast:
4	21:40565363-40575691..21:40718004-40719183	GM12878	blood:
5	chr21:40573985..40575559-chr8:146226955..146229907,2	MCF-7	breast:
6	chr21:40567725..40569767-chr21:40573079..40574814,2	MCF-7	breast:
7	chr21:40564573..40566805-chr21:40573736..40576146,2	K562	blood:

No data

Variant related genes	Relation type
BRWD1	TF binding region
ENSG00000185658	Chromatin interaction
ENSG00000255559	Chromatin interaction
ENSG00000272991	Chromatin interaction
ENSG00000237373	Chromatin interaction
ENSG00000183527	Chromatin interaction
ENSG00000205581	Chromatin interaction
ENSG00000196922	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 9 )

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

rs_ID	r²[population]
rs1011413	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1041439	0.86[ASN][1000 genomes]
rs11088471	0.89[CEU][hapmap];0.83[AMR][1000 genomes]
rs11088472	0.83[AMR][1000 genomes]
rs11910705	0.86[AMR][1000 genomes]
rs11911822	1.00[CEU][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12626405	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13050584	0.87[ASN][1000 genomes]
rs13051430	0.87[ASN][1000 genomes]
rs13052882	0.82[AFR][1000 genomes]
rs1571709	0.83[AFR][1000 genomes]
rs1888487	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1888488	0.88[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes]
rs2037925	0.92[CEU][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes]
rs2142111	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2150410	0.86[ASN][1000 genomes]
rs2150411	0.89[YRI][hapmap];0.86[AFR][1000 genomes]
rs2150412	0.87[ASN][1000 genomes]
rs2150413	0.86[ASW][hapmap]
rs2150414	0.86[ASW][hapmap]
rs2225425	0.85[ASN][1000 genomes]
rs2236437	0.86[ASN][1000 genomes]
rs2245455	0.92[CEU][hapmap];0.97[GIH][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2410104	0.86[ASN][1000 genomes]
rs2410123	0.96[CEU][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes]
rs2410124	0.83[AMR][1000 genomes]
rs2836930	0.89[YRI][hapmap];0.81[AFR][1000 genomes]
rs2836931	0.89[YRI][hapmap];0.83[AFR][1000 genomes]
rs2836956	0.86[ASW][hapmap]
rs2836958	0.86[ASW][hapmap]
rs2836959	0.93[ASW][hapmap];0.96[YRI][hapmap]
rs2836969	0.96[CEU][hapmap];0.81[JPT][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2836971	0.80[JPT][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2836975	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2836980	0.93[ASW][hapmap]
rs2836981	0.92[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes]
rs2836982	0.92[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes]
rs2836985	0.86[ASW][hapmap]
rs2836986	0.96[CEU][hapmap];0.83[AMR][1000 genomes]
rs2836987	0.92[CEU][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes]
rs2836988	0.96[CEU][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes]
rs34240248	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34436313	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs35182074	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35909862	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs36113648	0.82[AFR][1000 genomes]
rs371625	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs377098	0.96[CEU][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3831199	0.81[ASN][1000 genomes]
rs414850	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs418298	1.00[ASW][hapmap];0.92[CEU][hapmap];0.98[GIH][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs418359	1.00[ASW][hapmap];0.96[CEU][hapmap];0.98[GIH][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs419469	1.00[ASW][hapmap];0.92[CEU][hapmap];0.98[GIH][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs428602	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs429955	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs442972	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs452377	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4624474	0.96[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes]
rs4816620	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4817999	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4818001	0.89[YRI][hapmap];0.85[AFR][1000 genomes]
rs4818005	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4818015	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4818017	0.86[AMR][1000 genomes]
rs61300849	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6517522	0.93[ASW][hapmap]
rs6517524	0.87[ASN][1000 genomes]
rs6517525	0.87[ASN][1000 genomes]
rs6517535	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs719230	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7276774	0.90[CEU][hapmap];0.81[CHB][hapmap];0.84[JPT][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7278985	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7280326	0.82[AMR][1000 genomes]
rs7281853	0.92[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes]
rs7282029	0.86[ASN][1000 genomes]
rs7282604	1.00[ASW][hapmap];0.92[CEU][hapmap];0.98[GIH][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8127537	0.86[ASN][1000 genomes]
rs8127986	0.86[AMR][1000 genomes]
rs8130795	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8130854	0.84[AMR][1000 genomes]
rs8132143	0.89[YRI][hapmap]
rs8132295	0.93[ASW][hapmap]
rs8132333	0.93[ASW][hapmap]
rs8132424	0.93[ASW][hapmap];0.84[MKK][hapmap];0.89[YRI][hapmap]
rs9636957	0.84[AMR][1000 genomes]
rs997147	0.86[AMR][1000 genomes]
rs9974757	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9978775	0.86[AMR][1000 genomes]
rs9979483	0.80[AMR][1000 genomes]
rs9981301	0.96[CEU][hapmap];0.85[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9982111	0.86[AMR][1000 genomes];0.82[EUR][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	nsv1061831	chr21:40376316-40583555	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv544443	chr21:40376316-40583555	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1056683	chr21:40570023-40673210	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv459259	chr21:40571246-40701169	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv587480	chr21:40571246-40701169	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2183573	BRWD1	cis	Brain Pons	GTEx
rs2183573	PSMG1	cis	Skin Sun Exposed Lower leg	GTEx
rs2183573	BRWD1	cis	Temporal Cortex	GTEx
rs2183573	BRWD1	cis	Cerebellum	GTEx
rs2183573	PSMG1	cis	Esophagus Mucosa	GTEx
rs2183573	BRWD1	Cis_1M	lymphoblastoid	RTeQTL
rs2183573	BRWD1	cis	Frontal Cortex	GTEx
rs2183573	PSMG1	cis	lung	GTEx
rs2183573	PSMG1	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40556200-40576600	Weak transcription	Esophagus	oesophagus
2	chr21:40556200-40576600	Weak transcription	Pancreas	Pancrea
3	chr21:40556200-40602600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr21:40556600-40576600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr21:40563000-40640600	Strong transcription	Placenta	Placenta
6	chr21:40563000-40643600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr21:40563200-40581000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr21:40563400-40653400	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr21:40563400-40660000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr21:40563600-40575200	Strong transcription	HSMM	muscle
11	chr21:40563600-40588600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr21:40563600-40653600	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr21:40563800-40575400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr21:40564600-40612600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr21:40564800-40587800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr21:40565000-40581200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr21:40565000-40592600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr21:40565000-40654600	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr21:40565200-40579000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr21:40565200-40653600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr21:40565400-40574600	Strong transcription	Skeletal Muscle Female	skeletal muscle
22	chr21:40565400-40575400	Strong transcription	Primary hematopoietic stem cells	blood
23	chr21:40565400-40580800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr21:40565400-40604200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr21:40565400-40612600	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr21:40565400-40653600	Strong transcription	Dnd41	blood
27	chr21:40565600-40585600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr21:40565600-40590200	Strong transcription	Liver	Liver
29	chr21:40565600-40615000	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr21:40565800-40580600	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr21:40565800-40581400	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr21:40565800-40590600	Strong transcription	Fetal Thymus	thymus
33	chr21:40566000-40574600	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr21:40566000-40575000	Strong transcription	Primary B cells from peripheral blood	blood
35	chr21:40566000-40575200	Strong transcription	Duodenum Mucosa	Duodenum
36	chr21:40566000-40653600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr21:40566200-40575400	Strong transcription	NH-A	brain
38	chr21:40566200-40590600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
39	chr21:40566200-40590600	Strong transcription	Adipose Nuclei	Adipose
40	chr21:40566400-40575200	Strong transcription	Brain Inferior Temporal Lobe	brain
41	chr21:40566400-40575200	Strong transcription	Fetal Lung	lung
42	chr21:40566400-40580200	Strong transcription	K562	blood
43	chr21:40566400-40580800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr21:40566400-40613200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr21:40566600-40581200	Strong transcription	Fetal Muscle Trunk	muscle
46	chr21:40567400-40585400	Strong transcription	H1 Cell Line	embryonic stem cell
47	chr21:40567400-40592400	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr21:40567600-40574400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr21:40567600-40575000	Strong transcription	HepG2	liver
50	chr21:40567600-40580600	Strong transcription	GM12878-XiMat	blood

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