Variant report

Variant	rs2837454
Chromosome Location	chr21:41517445-41517446
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:41516165..41518166-chr21:41690706..41693774,3	MCF-7	breast:
2	chr21:41514680..41518758-chr21:41785744..41789812,5	MCF-7	breast:
3	chr21:41510559..41522908-chr21:41685904..41699622,30	MCF-7	breast:
4	chr21:41507356..41527112-chr21:41751014..41762921,70	MCF-7	breast:
5	chr21:41513242..41523747-chr21:41704483..41713607,25	MCF-7	breast:
6	chr21:41512480..41518922-chr21:41753940..41761141,21	MCF-7	breast:
7	chr21:41515156..41518019-chr21:41520939..41525508,4	MCF-7	breast:
8	chr21:41517119..41518686-chr21:41710416..41712657,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000235123	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10483063	1.00[YRI][hapmap]
rs11088509	0.88[AMR][1000 genomes]
rs11088510	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11701057	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11701139	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11702152	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11702402	0.85[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11911935	0.84[AMR][1000 genomes]
rs12151970	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12151971	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12152005	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12152078	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13046190	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13046360	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13046479	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1474493	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1474494	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.87[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2297264	0.85[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2297265	0.88[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2837452	0.85[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2837455	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2837456	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2837459	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2837460	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs36043003	0.83[ASN][1000 genomes]
rs3818650	0.90[AMR][1000 genomes]
rs4402848	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9977928	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9978469	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9979184	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9979203	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2837454	B3GALT5	cis	cerebellum	SCAN
rs2837454	MX2	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:41503000-41518400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr21:41505000-41526400	Weak transcription	Fetal Muscle Leg	muscle
3	chr21:41510800-41525800	Weak transcription	Brain Germinal Matrix	brain
4	chr21:41511000-41518600	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr21:41513000-41520600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr21:41513200-41523200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr21:41513400-41524400	Weak transcription	Fetal Brain Female	brain
8	chr21:41514200-41518200	Weak transcription	Fetal Muscle Trunk	muscle
9	chr21:41516800-41518400	Weak transcription	Fetal Brain Male	brain
10	chr21:41517200-41528800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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