Variant report

Variant	rs7279497
Chromosome Location	chr21:40531306-40531307
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:40529860..40532688-chr21:40545443..40547905,2	K562	blood:
2	21:40526994-40534295..21:40748850-40752541	K562	blood:
3	chr21:40530353..40532192-chr21:40535723..40538696,2	MCF-7	breast:
4	chr21:40524814..40527539-chr21:40530496..40533251,3	K562	blood:
5	chr21:40530945..40533694-chr21:40534297..40536978,4	K562	blood:

Variant related genes	Relation type
ENSG00000227406	Chromatin interaction
ENSG00000182093	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1029004	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11088466	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11088470	0.81[EUR][1000 genomes]
rs11700813	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11701805	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11910232	0.85[EUR][1000 genomes]
rs11911087	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12483559	0.84[EUR][1000 genomes]
rs12627205	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13049907	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1980407	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2037923	0.82[ASN][1000 genomes]
rs2056844	0.96[CEU][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.85[EUR][1000 genomes]
rs2070865	0.92[CEU][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap]
rs2150411	0.96[CEU][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2150413	1.00[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2150414	1.00[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2297256	0.88[ASW][hapmap];0.96[CEU][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.99[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2836922	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2836926	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836930	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836931	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836934	0.88[ASW][hapmap];1.00[CEU][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.98[LWK][hapmap];0.97[MKK][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2836940	0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2836942	0.96[CEU][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2836943	1.00[CEU][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2836945	1.00[CEU][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2836948	0.96[CEU][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2836949	0.96[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes]
rs2836952	1.00[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2836956	0.96[CEU][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs2836958	0.96[CEU][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs2836959	0.96[CEU][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs2836966	0.94[ASW][hapmap];1.00[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2836980	0.92[CEU][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs2836983	0.92[CEU][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes]
rs2836985	0.92[CEU][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap]
rs3171465	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34705151	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35769610	0.85[EUR][1000 genomes]
rs4816617	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4816618	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4818001	0.96[CEU][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4818019	0.80[EUR][1000 genomes]
rs59916147	0.86[EUR][1000 genomes]
rs62223011	0.86[EUR][1000 genomes]
rs62223039	0.83[EUR][1000 genomes]
rs6517518	0.87[CHB][hapmap];0.83[ASN][1000 genomes]
rs6517522	0.83[MEX][hapmap]
rs7276046	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7278297	0.96[CEU][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes]
rs7282582	0.88[CEU][hapmap];0.80[GIH][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap]
rs8127379	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8129595	0.81[EUR][1000 genomes]
rs8130162	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8130240	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8130320	0.88[ASW][hapmap];1.00[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.99[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8131132	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8132143	0.96[CEU][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8132424	0.96[CEU][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8133928	0.81[EUR][1000 genomes]
rs8134214	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8134843	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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
rs7279497	C21orf107	cis	multi-tissue	Pritchard
rs7279497	BRWD1	cis	multi-tissue	Pritchard
rs7279497	PSMG1	cis	parietal	SCAN
rs7279497	PSMG1	cis	lung	GTEx
rs7279497	BRWD1	cis	Frontal Cortex	GTEx
rs7279497	BRWD1	cis	Lymphoblastoid	GTEx
rs7279497	BRWD1	cis	cerebellum	SCAN
rs7279497	HMGN1	cis	lymphoblastoid	seeQTL
rs7279497	LOC643790	trans	multi-tissue	Pritchard
rs7279497	BRWD1	cis	Temporal Cortex	GTEx
rs7279497	HMGN1	cis	brain	seeQTL
rs7279497	DSCR2	cis	multi-tissue	Pritchard
rs7279497	WRB	cis	multi-tissue	Pritchard
rs7279497	BRWD1	cis	parietal	SCAN
rs7279497	BRWD1	cis	Brain Pons	GTEx
rs7279497	HMGN1	trans	brain	seeQTL
rs7279497	BRWD1	cis	lymphoblastoid	seeQTL
rs7279497	BRWD1	cis	Cerebellum	GTEx
rs7279497	PSMG1	cis	Artery Tibial	GTEx
rs7279497	HMGN1	cis	multi-tissue	Pritchard

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40530400-40531600	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr21:40530800-40531600	Enhancers	Monocytes-CD14+_RO01746	blood
3	chr21:40531000-40531400	Enhancers	Fetal Lung	lung
4	chr21:40531000-40531600	Enhancers	Osteobl	bone
5	chr21:40531000-40531800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr21:40531000-40532200	Enhancers	HSMMtube	muscle
7	chr21:40531000-40532400	Enhancers	Fetal Muscle Leg	muscle
8	chr21:40531000-40533400	Enhancers	HepG2	liver
9	chr21:40531200-40531600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr21:40531200-40531800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr21:40531200-40532200	Enhancers	Skeletal Muscle Male	skeletal muscle

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