Variant report

Variant	rs2837214
Chromosome Location	chr21:41149325-41149326
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:41144717..41146805-chr21:41147192..41149848,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1018352	0.94[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11701338	0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs12626544	0.81[JPT][hapmap]
rs1571712	0.93[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.91[TSI][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2205205	0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs2837183	0.81[JPT][hapmap]
rs2837205	0.97[LWK][hapmap];0.86[MKK][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes]
rs2837206	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2837208	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837213	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837215	1.00[ASW][hapmap];0.94[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];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837218	0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs2837219	0.85[ASN][1000 genomes]
rs2837221	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2837223	0.87[CHD][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs2837225	0.87[CHD][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs2837226	0.87[CHD][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs2837227	0.86[CHD][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs2837229	0.87[CHD][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs2837232	0.82[ASN][1000 genomes]
rs4337554	0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs447480	0.81[EUR][1000 genomes]
rs461583	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4818088	0.81[JPT][hapmap]
rs4818092	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4818093	0.87[CHB][hapmap]
rs4818094	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4818095	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7278733	0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs731592	0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs760285	0.86[CHD][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs760286	0.85[ASN][1000 genomes]
rs9305680	0.81[ASN][1000 genomes]
rs981653	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9974301	0.86[ASN][1000 genomes]
rs9978994	0.82[ASN][1000 genomes]
rs9983659	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1061454	chr21:40757973-41265404	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1057956	chr21:40907707-41393396	Enhancers Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv544444	chr21:40907707-41393396	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv1065086	chr21:41034806-41429078	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv544445	chr21:41034806-41429078	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv834099	chr21:41076873-41206030	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2837214	DSCR9	cis	parietal	SCAN
rs2837214	DSCAM	cis	cerebellum	SCAN
rs2837214	PSMG1	cis	cerebellum	SCAN
rs2837214	TMPRSS3	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:41137600-41152800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr21:41146000-41149400	Enhancers	Placenta	Placenta
3	chr21:41147600-41149400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr21:41148400-41149400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr21:41149000-41149400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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