Variant report

Variant	rs633705
Chromosome Location	chr21:40952583-40952584
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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:40951212..40954090-chr21:41083007..41085637,2	MCF-7	breast:
2	chr21:40902475..40904077-chr21:40952462..40954060,2	MCF-7	breast:
3	chr21:40951091..40953456-chr21:41032196..41036006,4	MCF-7	breast:
4	chr21:40816623..40819045-chr21:40951462..40953239,2	MCF-7	breast:
5	chr21:40894704..40896899-chr21:40951352..40952979,2	MCF-7	breast:
6	chr21:40899001..40900930-chr21:40949117..40954040,4	MCF-7	breast:
7	chr21:40950925..40952824-chr21:40985213..40987161,2	MCF-7	breast:
8	chr21:40950425..40953784-chr21:40975609..40978181,3	MCF-7	breast:
9	chr21:40950947..40952814-chr21:40953410..40955309,2	MCF-7	breast:
10	chr21:40951149..40953987-chr21:41066958..41068611,2	MCF-7	breast:
11	chr21:40933376..40935680-chr21:40951136..40954071,2	MCF-7	breast:
12	chr21:40951078..40953695-chr21:41039084..41042090,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000185437	Chromatin interaction
ENSG00000157578	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1076564	0.95[CHB][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs2837078	0.84[CHB][hapmap];0.81[CHD][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs2837084	0.86[ASN][1000 genomes]
rs2837085	0.89[CHB][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs2837087	0.95[CHB][hapmap];0.86[CHD][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs2837088	0.95[CHB][hapmap];0.86[CHD][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs2837089	0.95[CHB][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs2837090	0.95[CHB][hapmap];0.86[CHD][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs2837092	0.95[CHB][hapmap];0.87[JPT][hapmap];0.91[ASN][1000 genomes]
rs2898383	0.91[ASN][1000 genomes]
rs4816634	0.95[CHB][hapmap];0.86[CHD][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs4818060	0.92[ASN][1000 genomes]
rs484678	0.94[ASN][1000 genomes]
rs486465	0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs510750	0.94[ASN][1000 genomes]
rs517904	0.94[ASN][1000 genomes]
rs538329	0.93[ASN][1000 genomes]
rs572926	0.83[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs577473	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs585092	0.82[YRI][hapmap];0.80[AFR][1000 genomes]
rs586795	0.83[ASW][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.83[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs599045	0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs599377	0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs601732	0.84[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs614610	0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs617260	0.94[ASN][1000 genomes]
rs628045	0.94[ASN][1000 genomes]
rs630315	0.94[ASN][1000 genomes]
rs636599	0.83[ASW][hapmap];0.86[YRI][hapmap]
rs647448	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73358135	0.92[ASN][1000 genomes]
rs73358157	0.92[ASN][1000 genomes]
rs9712617	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1059868	chr21:40711535-41043291	Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	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
3	esv2756754	chr21:40857523-40966156	Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	esv2758820	chr21:40857523-40966156	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	esv34779	chr21:40884871-40977473	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv433457	chr21:40900348-40964553	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	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
8	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
9	esv17842	chr21:40918970-40965975	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv9863	chr21:40951227-40953760	Enhancers Weak transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs633705	TMPRSS2	cis	parietal	SCAN
rs633705	BRWD1	cis	parietal	SCAN
rs633705	RIPK4	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40948800-40952800	Weak transcription	Fetal Heart	heart
2	chr21:40948800-40955000	Weak transcription	Right Atrium	heart
3	chr21:40948800-40959800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr21:40949400-40959000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr21:40950800-40952800	Enhancers	Placenta	Placenta
6	chr21:40951800-40954000	Enhancers	Stomach Mucosa	stomach
7	chr21:40952000-40953600	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr21:40952400-40953000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links