Variant report

Variant	rs626856
Chromosome Location	chr21:40936014-40936015
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:40917372..40919952-chr21:40934813..40936673,2	MCF-7	breast:

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs12627708	1.00[JPT][hapmap]
rs1734930	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2037669	0.81[EUR][1000 genomes]
rs2837074	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2837083	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2989335	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs492140	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs503729	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs506387	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs516865	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs523372	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs526526	0.81[ASN][1000 genomes]
rs527343	0.81[ASN][1000 genomes]
rs528499	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs529409	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs538333	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs542531	0.81[ASN][1000 genomes]
rs551439	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs551624	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs551680	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.81[ASN][1000 genomes]
rs551830	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs554401	0.81[ASN][1000 genomes]
rs555963	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs561166	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs562285	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs563230	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs563259	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs564126	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs567837	0.81[ASN][1000 genomes]
rs568840	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs571227	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs579841	0.90[ASN][1000 genomes]
rs585092	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs59155174	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs596320	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs602107	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs606003	1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.80[TSI][hapmap]
rs606414	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs611039	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs611958	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs613758	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs617259	0.81[ASN][1000 genomes]
rs628995	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs629432	0.81[ASN][1000 genomes]
rs630270	0.81[ASN][1000 genomes]
rs631454	0.81[ASN][1000 genomes]
rs636599	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs644080	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap]
rs646823	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs650633	0.81[ASN][1000 genomes]
rs651607	0.81[ASN][1000 genomes]
rs657833	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs658066	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs665778	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.80[TSI][hapmap];0.81[ASN][1000 genomes]
rs689400	0.85[AFR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs626856	TMPRSS2	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40928600-40936800	Weak transcription	Brain Cingulate Gyrus	brain
2	chr21:40928600-40940200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr21:40931800-40940400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr21:40932600-40936800	Enhancers	Duodenum Mucosa	Duodenum
5	chr21:40933000-40937000	Enhancers	Fetal Heart	heart
6	chr21:40933600-40939000	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr21:40934200-40937200	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr21:40934200-40937400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr21:40934200-40937400	Enhancers	Brain Germinal Matrix	brain
10	chr21:40934400-40936400	Enhancers	Fetal Brain Female	brain
11	chr21:40934400-40937200	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr21:40934600-40936400	Enhancers	Pancreas	Pancrea
13	chr21:40934600-40936600	Enhancers	Fetal Muscle Leg	muscle
14	chr21:40935400-40937400	Enhancers	Fetal Brain Male	brain
15	chr21:40935600-40936400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr21:40935600-40939000	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr21:40935800-40936400	Enhancers	Fetal Muscle Trunk	muscle
18	chr21:40935800-40936400	Enhancers	Gastric	stomach
19	chr21:40935800-40936600	Enhancers	Duodenum Smooth Muscle	Duodenum
20	chr21:40935800-40936800	Weak transcription	Brain Anterior Caudate	brain
21	chr21:40936000-40936600	Enhancers	Colon Smooth Muscle	Colon
22	chr21:40936000-40937000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links