Variant report

Variant	rs516865
Chromosome Location	chr21:40937191-40937192
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	chr21:40932657..40935327-chr21:40936709..40939916,3	MCF-7	breast:
2	chr21:40936564..40938095-chr21:40947433..40949927,2	MCF-7	breast:

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1734930	1.00[ASN][1000 genomes]
rs2837074	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2837083	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2989335	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs492140	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs503729	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs506387	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs523372	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs526526	1.00[ASN][1000 genomes]
rs527343	1.00[ASN][1000 genomes]
rs528499	1.00[ASN][1000 genomes]
rs529409	1.00[ASN][1000 genomes]
rs538333	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs542531	1.00[ASN][1000 genomes]
rs551439	1.00[ASN][1000 genomes]
rs551624	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs551680	1.00[ASN][1000 genomes]
rs551830	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs554401	1.00[ASN][1000 genomes]
rs555963	1.00[ASN][1000 genomes]
rs561166	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs562285	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs563230	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs563259	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs564126	1.00[ASN][1000 genomes]
rs567837	1.00[ASN][1000 genomes]
rs568840	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs571227	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs579841	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs585092	1.00[ASN][1000 genomes]
rs59155174	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs596320	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs602107	1.00[ASN][1000 genomes]
rs611039	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs611958	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs613758	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs617259	1.00[ASN][1000 genomes]
rs626856	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs628995	1.00[ASN][1000 genomes]
rs629432	1.00[ASN][1000 genomes]
rs630270	1.00[ASN][1000 genomes]
rs631454	1.00[ASN][1000 genomes]
rs636599	1.00[ASN][1000 genomes]
rs646823	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs650633	1.00[ASN][1000 genomes]
rs651607	1.00[ASN][1000 genomes]
rs657833	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs658066	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs665778	1.00[ASN][1000 genomes]
rs689400	0.95[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

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40928600-40940200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr21:40931800-40940400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr21:40933600-40939000	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr21:40934200-40937200	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr21:40934200-40937400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr21:40934200-40937400	Enhancers	Brain Germinal Matrix	brain
7	chr21:40934400-40937200	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr21:40935400-40937400	Enhancers	Fetal Brain Male	brain
9	chr21:40935600-40939000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr21:40936400-40937200	Enhancers	Stomach Smooth Muscle	stomach
11	chr21:40936400-40940200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr21:40936400-40940200	Weak transcription	Pancreas	Pancrea
13	chr21:40936800-40937200	Enhancers	Brain Anterior Caudate	brain
14	chr21:40936800-40937200	Enhancers	Brain Cingulate Gyrus	brain
15	chr21:40936800-40937200	Enhancers	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links