Variant report

Variant	rs419469
Chromosome Location	chr21:40537234-40537235
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	21:40535091-40537322..21:40757151-40764378	GM12878	blood:
2	chr21:40530353..40532192-chr21:40535723..40538696,2	MCF-7	breast:
3	chr21:40534864..40537337-chr21:40540303..40542416,2	K562	blood:

Variant related genes	Relation type
ENSG00000182093	Chromatin interaction

Extended variants
information (count: 116 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs1011413	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10154057	0.81[ASN][1000 genomes]
rs11088471	0.90[CEU][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes]
rs11088472	0.83[AMR][1000 genomes]
rs11910705	0.82[AMR][1000 genomes]
rs11911112	0.80[AFR][1000 genomes]
rs11911149	0.82[AFR][1000 genomes]
rs11911822	0.96[CEU][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12482181	0.84[MEX][hapmap]
rs12626405	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13050247	0.83[ASN][1000 genomes]
rs14194	0.83[MEX][hapmap]
rs1571709	0.90[YRI][hapmap]
rs1888487	0.84[AMR][1000 genomes]
rs1888488	0.85[ASW][hapmap];0.89[CEU][hapmap];0.91[GIH][hapmap];0.87[JPT][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes]
rs1980407	0.85[AFR][1000 genomes]
rs2037925	0.84[ASW][hapmap];0.88[CEU][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes]
rs2142111	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2150411	1.00[YRI][hapmap]
rs2150413	0.92[ASW][hapmap]
rs2150414	0.92[ASW][hapmap]
rs2183573	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]
rs2245455	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2410123	0.85[ASW][hapmap];0.89[CEU][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes]
rs2410124	0.83[AMR][1000 genomes]
rs2836924	0.82[AFR][1000 genomes]
rs2836925	0.84[MEX][hapmap]
rs2836929	0.84[MEX][hapmap]
rs2836930	1.00[YRI][hapmap]
rs2836931	1.00[YRI][hapmap]
rs2836932	0.84[MEX][hapmap]
rs2836956	0.92[ASW][hapmap]
rs2836958	0.92[ASW][hapmap]
rs2836959	0.92[ASW][hapmap];0.96[YRI][hapmap]
rs2836969	1.00[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2836971	0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2836975	1.00[ASW][hapmap];0.96[CEU][hapmap];0.82[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.89[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2836980	0.93[ASW][hapmap];0.89[YRI][hapmap]
rs2836981	0.85[ASW][hapmap];0.92[CEU][hapmap];0.91[GIH][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes]
rs2836982	0.85[ASW][hapmap];0.92[CEU][hapmap];0.91[GIH][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes]
rs2836983	0.89[YRI][hapmap]
rs2836985	0.92[ASW][hapmap]
rs2836986	0.92[CEU][hapmap];0.83[AMR][1000 genomes]
rs2836987	0.85[ASW][hapmap];0.92[CEU][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes]
rs2836988	0.85[ASW][hapmap];0.89[CEU][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes]
rs34240248	0.83[AMR][1000 genomes]
rs34436313	0.83[AMR][1000 genomes]
rs35909862	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs371625	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs377098	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs383967	0.83[ASN][1000 genomes]
rs391062	0.85[CHB][hapmap];0.83[ASN][1000 genomes]
rs413078	0.85[CHB][hapmap];0.83[ASN][1000 genomes]
rs414850	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs418298	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs418359	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs425988	0.83[ASN][1000 genomes]
rs428602	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]
rs429955	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs442972	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs444130	0.83[ASN][1000 genomes]
rs452377	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs452776	0.83[ASN][1000 genomes]
rs4624474	0.85[ASW][hapmap];0.89[CEU][hapmap];0.91[GIH][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes]
rs4816620	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4817996	0.82[AFR][1000 genomes]
rs4817999	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4818001	1.00[YRI][hapmap]
rs4818005	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4818015	1.00[ASW][hapmap];0.96[CEU][hapmap];0.82[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4818017	0.84[AMR][1000 genomes]
rs61300849	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6517513	0.82[AFR][1000 genomes]
rs6517514	0.82[AFR][1000 genomes]
rs6517519	0.84[MEX][hapmap]
rs6517520	0.85[CHB][hapmap];0.83[ASN][1000 genomes]
rs6517522	0.92[ASW][hapmap];0.90[YRI][hapmap]
rs6517535	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
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]
rs68090597	0.83[AFR][1000 genomes]
rs68114370	0.83[ASN][1000 genomes]
rs719230	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7276774	1.00[CEU][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7278985	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7280326	0.82[AMR][1000 genomes]
rs7280375	0.84[MEX][hapmap]
rs7281853	0.85[ASW][hapmap];0.92[CEU][hapmap];0.91[GIH][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes]
rs7282604	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8127986	0.84[AMR][1000 genomes]
rs8128191	0.90[YRI][hapmap];0.82[AFR][1000 genomes]
rs8130240	0.84[AFR][1000 genomes]
rs8130795	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8130854	0.84[AMR][1000 genomes]
rs8132143	1.00[YRI][hapmap]
rs8132295	0.92[ASW][hapmap];0.81[MKK][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes]
rs8132333	0.92[ASW][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes]
rs8132419	0.82[AFR][1000 genomes]
rs8132424	0.93[ASW][hapmap];1.00[YRI][hapmap]
rs8132568	0.80[AFR][1000 genomes]
rs8134214	0.87[AFR][1000 genomes]
rs9636957	0.84[AMR][1000 genomes]
rs997147	0.84[AMR][1000 genomes]
rs9974757	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9978775	0.84[AMR][1000 genomes]
rs9979483	0.80[AMR][1000 genomes]
rs9981301	0.92[CEU][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes]
rs9982111	0.86[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:20)

SNP	Gene	Cis/trans	Tissue	Source
rs419469	BRWD1	cis	multi-tissue	Pritchard
rs419469	BRWD1	cis	parietal	SCAN
rs419469	DSCR2	cis	multi-tissue	Pritchard
rs419469	PSMG1	cis	Skin Sun Exposed Lower leg	GTEx
rs419469	PSMG1	cis	Esophagus Mucosa	GTEx
rs419469	C21orf107	cis	multi-tissue	Pritchard
rs419469	HMGN1	cis	multi-tissue	Pritchard
rs419469	BRWD1	cis	Temporal Cortex	GTEx
rs419469	BRWD1	cis	Frontal Cortex	GTEx
rs419469	DSCR2	cis	lesional skin	skin_eQTL
rs419469	PSMG1	cis	Artery Tibial	GTEx
rs419469	LOC643790	trans	multi-tissue	Pritchard
rs419469	DSCR2	cis	normal skin	skin_eQTL
rs419469	PSMG1	cis	Nerve Tibial	GTEx
rs419469	BRWD1	cis	Brain Pons	GTEx
rs419469	PSMG1	cis	parietal	SCAN
rs419469	BRWD1	cis	Cerebellum	GTEx
rs419469	BRWD1	cis	Lymphoblastoid	GTEx
rs419469	PSMG1	cis	lung	GTEx
rs419469	BRWD1	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40533600-40545400	Weak transcription	HUVEC	blood vessel
2	chr21:40536200-40537400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr21:40536400-40541200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr21:40536800-40541200	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr21:40537000-40537400	ZNF genes & repeats	Aorta	Aorta
6	chr21:40537200-40541200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr21:40537200-40541200	Weak transcription	Adipose Nuclei	Adipose
8	chr21:40537200-40541200	Weak transcription	HSMMtube	muscle
9	chr21:40537200-40542800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr21:40537200-40543000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr21:40537200-40543000	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr21:40537200-40543000	Weak transcription	Lung	lung
13	chr21:40537200-40543000	Weak transcription	Pancreas	Pancrea

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