Variant report

Variant	rs1997543
Chromosome Location	chr21:40974288-40974289
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F6	chr21:40974147-40974577	H1-hESC	embryonic stem cell:	n/a	chr21:40974217-40974226
2	POLR2A	chr21:40974194-40974431	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:40974039..40977306-chr21:40982060..40986633,4	MCF-7	breast:
2	chr21:40973024..40975835-chr21:41005421..41007852,2	MCF-7	breast:

Variant related genes	Relation type
C21orf88	TF binding region
ENSG00000184809	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1076564	0.82[CEU][hapmap];0.80[JPT][hapmap];0.85[AMR][1000 genomes]
rs11088487	0.95[ASN][1000 genomes]
rs2222580	0.84[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2837078	0.82[CEU][hapmap];0.80[JPT][hapmap];0.81[AMR][1000 genomes]
rs2837084	0.85[AMR][1000 genomes]
rs2837085	0.82[CEU][hapmap];0.80[JPT][hapmap];0.85[AMR][1000 genomes]
rs2837087	0.82[CEU][hapmap];0.80[JPT][hapmap];0.85[AMR][1000 genomes]
rs2837088	0.82[CEU][hapmap];0.80[JPT][hapmap];0.85[AMR][1000 genomes]
rs2837089	0.82[CEU][hapmap];0.80[JPT][hapmap];0.85[AMR][1000 genomes]
rs2837090	0.82[CEU][hapmap];0.80[JPT][hapmap]
rs2837092	0.80[JPT][hapmap]
rs2837096	1.00[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41455449	0.84[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4816633	0.81[AMR][1000 genomes]
rs4816634	0.80[JPT][hapmap]
rs4818054	0.81[AMR][1000 genomes]
rs4818057	0.81[AMR][1000 genomes]
rs4818061	0.88[ASN][1000 genomes]
rs59004308	0.95[ASN][1000 genomes]
rs914160	0.82[CEU][hapmap];0.80[JPT][hapmap]
rs9712617	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
4	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
5	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

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40965600-40976400	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr21:40970200-40976600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr21:40970200-40982400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr21:40970400-40976800	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr21:40970400-40979800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr21:40970400-40981800	Weak transcription	Pancreas	Pancrea
7	chr21:40970800-40984600	Weak transcription	Right Atrium	heart
8	chr21:40972600-40974400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr21:40973400-40974400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr21:40973400-40974400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr21:40973400-40974400	Enhancers	Placenta Amnion	Placenta Amnion
12	chr21:40973400-40982400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr21:40973800-40974400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr21:40973800-40974600	Enhancers	Duodenum Mucosa	Duodenum
15	chr21:40974000-40974400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr21:40974000-40976800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr21:40974000-40982200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr21:40974200-40976600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr21:40974200-40980400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr21:40974200-40980600	Weak transcription	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links