Variant report

Variant	rs2837232
Chromosome Location	chr21:41179213-41179214
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:41178535..41181156-chr21:41183661..41185952,2	MCF-7	breast:
2	chr21:41164154..41166617-chr21:41178349..41181058,2	MCF-7	breast:
3	chr21:41173962..41176069-chr21:41178013..41180055,3	MCF-7	breast:

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

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

rs_ID	r²[population]
rs1004663	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1018352	0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs10470190	0.86[JPT][hapmap]
rs11701338	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12626544	0.82[CHD][hapmap];0.90[JPT][hapmap]
rs12627540	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1571712	0.85[CHD][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs1984023	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2205205	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2244761	0.88[EUR][1000 genomes];0.85[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];0.81[ASN][1000 genomes]
rs2837208	0.85[CHD][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs2837213	0.82[ASN][1000 genomes]
rs2837214	0.87[CHD][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs2837215	0.85[CHD][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs2837218	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2837219	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2837221	0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2837223	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2837225	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2837226	0.91[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2837227	0.84[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2837229	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2837246	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2837247	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2837249	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2837253	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2837257	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2837258	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2837259	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2837260	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4337554	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs461583	0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs4816652	0.86[JPT][hapmap]
rs4816653	0.86[JPT][hapmap]
rs4818088	0.90[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4818092	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs4818094	0.85[CHD][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs4818095	0.82[ASN][1000 genomes]
rs4818096	0.81[CEU][hapmap]
rs4818098	0.85[AFR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7277375	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7278733	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs731592	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs741866	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs760285	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs760286	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9305680	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs981653	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs9974301	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9974413	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9978994	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9979170	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9979395	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9980807	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9980954	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9982214	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9982243	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9982859	0.90[EUR][1000 genomes];0.87[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
rs2837232	TMPRSS3	cis	cerebellum	SCAN
rs2837232	B3GALT5	cis	parietal	SCAN
rs2837232	MORC3	cis	parietal	SCAN

Chromatin state (count:12 , 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	chr21:41176800-41184200	Weak transcription	Fetal Brain Male	brain
4	chr21:41177000-41180800	Weak transcription	Fetal Heart	heart
5	chr21:41178000-41179400	Weak transcription	Fetal Lung	lung
6	chr21:41178000-41182200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr21:41178600-41180600	Enhancers	Placenta	Placenta
8	chr21:41179200-41179400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr21:41179200-41179400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
10	chr21:41179200-41179600	Enhancers	Colon Smooth Muscle	Colon
11	chr21:41179200-41180800	Enhancers	Gastric	stomach
12	chr21:41179200-41181000	Enhancers	Stomach Mucosa	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links