Variant report

Variant	rs2837227
Chromosome Location	chr21:41172166-41172167
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1004663	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1018352	0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs10470190	0.86[JPT][hapmap]
rs11701338	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12626544	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs12627540	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1571712	0.87[CHD][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs1984023	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2205205	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2244761	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2837175	0.86[JPT][hapmap]
rs2837176	0.86[JPT][hapmap]
rs2837178	0.86[JPT][hapmap]
rs2837183	0.90[JPT][hapmap]
rs2837206	0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs2837208	0.87[CHD][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs2837213	0.85[ASN][1000 genomes]
rs2837214	0.86[CHD][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs2837215	0.87[CHD][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs2837218	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2837219	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837221	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837223	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837225	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837226	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837229	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2837232	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2837246	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2837247	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2837249	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2837253	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2837257	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2837258	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2837259	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2837260	0.84[EUR][1000 genomes]
rs4337554	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs461583	0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs4816652	0.86[JPT][hapmap]
rs4816653	0.86[JPT][hapmap]
rs4818088	0.90[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4818092	0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs4818094	0.87[CHD][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs4818095	0.85[ASN][1000 genomes]
rs4818096	0.81[CEU][hapmap]
rs4818098	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7277375	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7278733	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs731592	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs741866	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs760285	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs760286	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9305680	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs981653	0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs9974301	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9974413	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9978994	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9979170	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9979395	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9980807	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9980954	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9982214	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9982243	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9982859	0.88[EUR][1000 genomes];0.85[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2837227	B3GALT5	cis	parietal	SCAN
rs2837227	MORC3	cis	parietal	SCAN
rs2837227	TMPRSS3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:41161400-41180000	Weak transcription	Pancreas	Pancrea
2	chr21:41164200-41185600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr21:41166200-41173200	Weak transcription	Placenta	Placenta
4	chr21:41171000-41176400	Weak transcription	Left Ventricle	heart
5	chr21:41171200-41176000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr21:41171400-41172600	Weak transcription	Fetal Stomach	stomach
7	chr21:41171800-41174000	Weak transcription	Fetal Heart	heart
8	chr21:41171800-41176400	Weak transcription	Fetal Brain Male	brain

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