Variant report

Variant	rs428602
Chromosome Location	chr21:40547004-40547005
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr21:40546911-40548103	SK-N-SH	brain:	n/a	n/a
2	CTCF	chr21:40546960-40547110	GM12864	blood:	n/a	n/a
3	RAD21	chr21:40546976-40547408	SK-N-SH_RA	brain:	n/a	n/a
4	CTCF	chr21:40546920-40547070	HVMF	connective:	n/a	n/a
5	CTCF	chr21:40546940-40547090	WI-38	lung:	n/a	n/a
6	RAD21	chr21:40546595-40547838	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr21:40546956-40547156	HepG2	liver:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:40105428..40106530-chr21:40546782..40547826,4	MCF-7	breast:
2	chr21:40542935..40544954-chr21:40544958..40548517,4	MCF-7	breast:
3	chr21:39731389..39731939-chr21:40546750..40547723,2	MCF-7	breast:
4	chr21:39877751..39878284-chr21:40546921..40547774,2	K562	blood:
5	chr21:40529860..40532688-chr21:40545443..40547905,2	K562	blood:
6	chr21:40544824..40547305-chr21:40554591..40556677,3	MCF-7	breast:

No data

Variant related genes	Relation type
PCBP2P1	TF binding region
ENSG00000272991	Chromatin interaction
ENSG00000235701	Chromatin interaction
ENSG00000183527	Chromatin interaction

Extended variants
information (count: 113 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs1011413	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10154057	0.81[ASN][1000 genomes]
rs11088471	0.90[CEU][hapmap];0.83[YRI][hapmap];0.80[AMR][1000 genomes]
rs11088472	0.80[AMR][1000 genomes]
rs11911822	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12482181	0.89[YRI][hapmap];0.81[AFR][1000 genomes]
rs12626405	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13048178	0.80[AFR][1000 genomes]
rs13050247	0.83[ASN][1000 genomes]
rs13625	0.89[YRI][hapmap]
rs14194	0.89[YRI][hapmap];0.82[AFR][1000 genomes]
rs1541102	0.89[YRI][hapmap]
rs1888487	0.82[AMR][1000 genomes]
rs1888488	0.88[CEU][hapmap];0.87[JPT][hapmap];0.96[YRI][hapmap];0.83[AMR][1000 genomes]
rs1984022	0.90[YRI][hapmap]
rs2026265	0.90[YRI][hapmap]
rs2037925	0.88[CEU][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes]
rs2142111	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2150413	1.00[YRI][hapmap]
rs2150414	1.00[YRI][hapmap]
rs2150415	0.87[YRI][hapmap]
rs2183573	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2234543	0.89[YRI][hapmap]
rs2245455	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2410123	0.92[CEU][hapmap];0.87[JPT][hapmap];0.85[YRI][hapmap];0.81[AMR][1000 genomes]
rs2410124	0.80[AMR][1000 genomes]
rs2836925	0.89[YRI][hapmap]
rs2836929	0.89[YRI][hapmap]
rs2836932	0.89[YRI][hapmap];0.81[AFR][1000 genomes]
rs2836933	0.90[YRI][hapmap]
rs2836956	1.00[YRI][hapmap]
rs2836957	0.90[YRI][hapmap]
rs2836958	1.00[YRI][hapmap]
rs2836964	0.89[YRI][hapmap]
rs2836965	0.89[YRI][hapmap]
rs2836967	0.90[YRI][hapmap]
rs2836968	0.89[YRI][hapmap]
rs2836969	1.00[CEU][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2836971	0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2836974	0.89[YRI][hapmap]
rs2836975	0.96[CEU][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2836981	0.92[CEU][hapmap];0.87[JPT][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes]
rs2836982	0.92[CEU][hapmap];0.87[JPT][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes]
rs2836986	0.93[CEU][hapmap];0.83[YRI][hapmap];0.80[AMR][1000 genomes]
rs2836987	0.92[CEU][hapmap];0.87[JPT][hapmap];0.85[YRI][hapmap];0.81[AMR][1000 genomes]
rs2836988	0.92[CEU][hapmap];0.87[JPT][hapmap];0.81[AMR][1000 genomes]
rs34176878	0.81[AFR][1000 genomes]
rs34240248	0.80[AMR][1000 genomes]
rs34436313	0.80[AMR][1000 genomes]
rs35909862	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs371625	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs377098	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs383967	0.83[ASN][1000 genomes]
rs391062	0.86[CHB][hapmap];0.83[ASN][1000 genomes]
rs413078	0.85[CHB][hapmap];0.83[ASN][1000 genomes]
rs414850	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs418298	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs418359	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs419469	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs425988	0.83[ASN][1000 genomes]
rs429955	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs442972	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs444130	0.83[ASN][1000 genomes]
rs452377	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs452776	0.83[ASN][1000 genomes]
rs4624474	0.92[CEU][hapmap];0.87[JPT][hapmap];0.96[YRI][hapmap];0.80[AMR][1000 genomes]
rs4816620	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4817999	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4818005	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4818015	0.96[CEU][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4818017	0.82[AMR][1000 genomes]
rs61300849	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6517519	0.89[YRI][hapmap]
rs6517520	0.86[CHB][hapmap];0.83[ASN][1000 genomes]
rs6517521	0.81[AFR][1000 genomes]
rs6517523	0.89[YRI][hapmap];0.80[AFR][1000 genomes]
rs6517526	0.89[YRI][hapmap]
rs6517535	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6517538	0.89[YRI][hapmap]
rs6650847	0.83[ASN][1000 genomes]
rs66519408	0.83[ASN][1000 genomes]
rs66746936	0.83[ASN][1000 genomes]
rs67212994	0.83[ASN][1000 genomes]
rs67382266	0.81[ASN][1000 genomes]
rs67649754	0.83[ASN][1000 genomes]
rs68086041	0.81[ASN][1000 genomes]
rs68114370	0.83[ASN][1000 genomes]
rs719230	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7276774	1.00[CEU][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7278297	1.00[YRI][hapmap]
rs7278985	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7280375	0.89[YRI][hapmap];0.83[AFR][1000 genomes]
rs7281853	0.92[CEU][hapmap];0.87[JPT][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes]
rs7282604	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7283516	0.83[YRI][hapmap]
rs73221193	0.80[AFR][1000 genomes]
rs8127087	0.90[YRI][hapmap]
rs8127986	0.82[AMR][1000 genomes]
rs8128026	0.88[YRI][hapmap]
rs8128102	0.83[YRI][hapmap]
rs8130795	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8130854	0.81[AMR][1000 genomes]
rs8130984	0.93[YRI][hapmap]
rs8132285	0.90[YRI][hapmap]
rs9636957	0.81[AMR][1000 genomes]
rs997147	0.82[AMR][1000 genomes]
rs9974757	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9978775	0.82[AMR][1000 genomes]
rs9981301	0.92[CEU][hapmap];0.87[JPT][hapmap];0.96[YRI][hapmap]
rs9982111	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9982122	0.85[CHB][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs428602	BRWD1	cis	Lymphoblastoid	GTEx
rs428602	PSMG1	cis	Nerve Tibial	GTEx
rs428602	C21orf107	cis	multi-tissue	Pritchard
rs428602	PSMG1	cis	Esophagus Mucosa	GTEx
rs428602	BRWD1	Cis_1M	lymphoblastoid	RTeQTL
rs428602	BRWD1	cis	Temporal Cortex	GTEx
rs428602	PSMG1	cis	Artery Tibial	GTEx
rs428602	PSMG1	cis	Skin Sun Exposed Lower leg	GTEx
rs428602	BRWD1	cis	Brain Pons	GTEx
rs428602	DSCR2	cis	normal skin	skin_eQTL
rs428602	BRWD1	cis	Frontal Cortex	GTEx
rs428602	BRWD1	cis	Cerebellum	GTEx
rs428602	PSMG1	cis	lung	GTEx
rs428602	DSCR2	cis	lesional skin	skin_eQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40537600-40553800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr21:40538800-40550400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr21:40539000-40550800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr21:40539600-40554000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr21:40539800-40554000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr21:40540200-40554200	Weak transcription	Psoas Muscle	Psoas
7	chr21:40541000-40547600	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr21:40541200-40547800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr21:40541200-40548400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr21:40541200-40550600	Strong transcription	Dnd41	blood
11	chr21:40541200-40552600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr21:40541200-40552800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr21:40541200-40553000	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr21:40541200-40553000	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr21:40541200-40553600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr21:40541200-40553800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr21:40541200-40554000	Weak transcription	Brain Substantia Nigra	brain
18	chr21:40541400-40553000	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr21:40541600-40553800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr21:40541600-40554000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr21:40541600-40554000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr21:40541600-40554000	Weak transcription	Colon Smooth Muscle	Colon
23	chr21:40541800-40554400	Weak transcription	Brain Germinal Matrix	brain
24	chr21:40542000-40554000	Weak transcription	Rectal Smooth Muscle	rectum
25	chr21:40542000-40554000	Weak transcription	Stomach Mucosa	stomach
26	chr21:40542200-40551600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr21:40542400-40548600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr21:40542400-40554400	Weak transcription	Right Atrium	heart
29	chr21:40542800-40547400	Weak transcription	Fetal Heart	heart
30	chr21:40542800-40554000	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr21:40543000-40547600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr21:40543000-40547800	Strong transcription	Muscle Satellite Cultured Cells	--
33	chr21:40543000-40548000	Strong transcription	Fetal Intestine Small	intestine
34	chr21:40543000-40549400	Strong transcription	HepG2	liver
35	chr21:40543000-40552400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr21:40543000-40552400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr21:40543000-40552600	Strong transcription	Osteobl	bone
38	chr21:40543200-40548200	Strong transcription	NH-A	brain
39	chr21:40543200-40549000	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr21:40543200-40549400	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr21:40543200-40551800	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr21:40543400-40554000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr21:40543600-40553200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr21:40543800-40550600	Weak transcription	Fetal Kidney	kidney
45	chr21:40543800-40553200	Weak transcription	Small Intestine	intestine
46	chr21:40543800-40554000	Weak transcription	Brain Cingulate Gyrus	brain
47	chr21:40543800-40554000	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr21:40543800-40554200	Weak transcription	Right Ventricle	heart
49	chr21:40543800-40554600	Weak transcription	Left Ventricle	heart
50	chr21:40544000-40547600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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