Variant report

Variant	rs2836922
Chromosome Location	chr21:40516308-40516309
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:40500620..40503419-chr21:40514957..40517352,2	MCF-7	breast:
2	chr21:40187682..40190648-chr21:40515051..40517560,2	K562	blood:
3	chr21:40515045..40517446-chr21:40522211..40524876,3	MCF-7	breast:

Extended variants
information (count: 48 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11088466	0.82[EUR][1000 genomes]
rs11700813	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1980407	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2056844	0.93[CEU][hapmap];0.80[CHB][hapmap];0.81[JPT][hapmap]
rs2070865	0.88[CEU][hapmap]
rs2150411	0.93[CEU][hapmap];0.80[CHB][hapmap];0.81[JPT][hapmap];0.85[EUR][1000 genomes]
rs2150413	0.96[CEU][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes]
rs2150414	0.96[CEU][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes]
rs2297256	0.92[CEU][hapmap];0.85[JPT][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2836926	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2836930	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2836931	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2836934	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs2836940	0.81[EUR][1000 genomes]
rs2836942	0.93[CEU][hapmap];0.80[CHB][hapmap];0.81[JPT][hapmap];0.81[EUR][1000 genomes]
rs2836943	0.96[CEU][hapmap];0.81[JPT][hapmap];0.82[EUR][1000 genomes]
rs2836945	0.96[CEU][hapmap];0.80[CHB][hapmap];0.81[JPT][hapmap];0.82[EUR][1000 genomes]
rs2836948	0.93[CEU][hapmap];0.80[CHB][hapmap];0.81[JPT][hapmap];0.81[EUR][1000 genomes]
rs2836949	0.93[CEU][hapmap];0.85[JPT][hapmap]
rs2836952	0.96[CEU][hapmap]
rs2836956	0.92[CEU][hapmap];0.85[JPT][hapmap]
rs2836958	0.92[CEU][hapmap];0.84[JPT][hapmap]
rs2836959	0.92[CEU][hapmap]
rs2836966	0.96[CEU][hapmap];0.85[JPT][hapmap]
rs2836980	0.88[CEU][hapmap]
rs2836983	0.89[CEU][hapmap];0.80[CHB][hapmap]
rs2836985	0.88[CEU][hapmap]
rs3171465	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34705151	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4816617	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4816618	0.81[EUR][1000 genomes]
rs4818001	0.93[CEU][hapmap];0.80[CHB][hapmap];0.81[JPT][hapmap];0.84[EUR][1000 genomes]
rs6517518	0.87[CHB][hapmap]
rs7276046	0.82[EUR][1000 genomes]
rs7278297	0.93[CEU][hapmap];0.80[CHB][hapmap];0.81[JPT][hapmap]
rs7279497	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7282582	0.84[CEU][hapmap]
rs8127379	0.82[EUR][1000 genomes]
rs8130240	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8130320	0.96[CEU][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes]
rs8131132	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8132143	0.93[CEU][hapmap];0.80[CHB][hapmap];0.81[JPT][hapmap];0.82[EUR][1000 genomes]
rs8132424	0.92[CEU][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes]
rs8134214	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8134843	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	esv3395554	chr21:40512728-40517052	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2836922	HMGN1	cis	multi-tissue	Pritchard
rs2836922	BRWD1	cis	Cerebellum	GTEx
rs2836922	BRWD1	cis	Temporal Cortex	GTEx
rs2836922	BRWD1	Cis_1M	lymphoblastoid	RTeQTL
rs2836922	PSMG1	cis	Artery Tibial	GTEx
rs2836922	BRWD1	cis	Frontal Cortex	GTEx
rs2836922	BRWD1	cis	Lymphoblastoid	GTEx
rs2836922	HMGN1	Cis_1M	lymphoblastoid	RTeQTL
rs2836922	BRWD1	cis	Brain Pons	GTEx
rs2836922	C21orf107	cis	multi-tissue	Pritchard

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40514200-40517000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr21:40514200-40520200	Weak transcription	Psoas Muscle	Psoas
3	chr21:40515000-40516400	Enhancers	Fetal Muscle Leg	muscle
4	chr21:40515800-40516400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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