Variant report

Variant	rs506382
Chromosome Location	chr21:40977826-40977827
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:5)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:40975922..40977945-chr21:40981394..40984393,2	MCF-7	breast:
2	chr21:40950425..40953784-chr21:40975609..40978181,3	MCF-7	breast:
3	chr21:40976514..40978882-chr21:40987659..40990131,2	MCF-7	breast:
4	chr21:40968353..40970588-chr21:40974618..40978683,3	MCF-7	breast:
5	chr21:40898411..40901316-chr21:40977081..40979354,2	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C21orf88-1	chr21:40976387-40978276	NONHSAT082200
2	lnc-C21orf88-1	chr21:40977534-40978274	NR_026543

No data

Variant related genes	Relation type
ENSG00000184809	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs13048647	0.87[ASN][1000 genomes]
rs1524931	0.95[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs1734932	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1880516	0.86[ASN][1000 genomes]
rs2091883	0.95[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs473907	0.92[ASN][1000 genomes]
rs478524	0.93[ASN][1000 genomes]
rs502507	0.95[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.93[ASN][1000 genomes]
rs511415	0.86[CHB][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.93[ASN][1000 genomes]
rs582539	0.93[ASN][1000 genomes]
rs760163	0.95[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs8127751	0.95[CHB][hapmap];0.81[CHD][hapmap];0.85[JPT][hapmap]
rs856992	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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
4	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs506382	TFF3	cis	cerebellum	SCAN
rs506382	RIPK4	cis	cerebellum	SCAN
rs506382	MORC3	cis	cerebellum	SCAN
rs506382	RIPK4	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40970200-40982400	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr21:40970400-40979800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr21:40970400-40981800	Weak transcription	Pancreas	Pancrea
4	chr21:40970800-40984600	Weak transcription	Right Atrium	heart
5	chr21:40973400-40982400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr21:40974000-40982200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr21:40974200-40980400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr21:40974200-40980600	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr21:40974400-40980600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr21:40974400-40982200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr21:40974400-40982400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr21:40974400-40982600	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr21:40975600-40981400	Weak transcription	Duodenum Mucosa	Duodenum
14	chr21:40976400-40981200	Strong transcription	H1 Cell Line	embryonic stem cell
15	chr21:40976600-40978000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr21:40976600-40978200	Strong transcription	H9 Cell Line	embryonic stem cell
17	chr21:40976800-40978200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
18	chr21:40976800-40983200	Weak transcription	Brain Anterior Caudate	brain
19	chr21:40977200-40980800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr21:40977400-40982200	Weak transcription	HUES48 Cell Line	embryonic stem cell

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