Variant report

Variant	rs511415
Chromosome Location	chr21:40970376-40970377
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:40963714..40965931-chr21:40968819..40971403,2	K562	blood:
2	chr21:40968353..40970588-chr21:40974618..40978683,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C21orf88-1	chr21:40969031-40972206	NONHSAT082200

Extended variants
information (count: 18 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs13048647	0.92[ASN][1000 genomes]
rs1524931	0.91[CHB][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs1734932	0.86[CHB][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap];0.92[ASN][1000 genomes]
rs1880516	0.93[ASN][1000 genomes]
rs2091883	0.91[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs473907	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs478524	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs502507	0.96[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs506382	0.86[CHB][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.93[ASN][1000 genomes]
rs582539	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs760163	0.91[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs8127751	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs856992	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs511415	RIPK4	cis	cerebellum	SCAN
rs511415	BRWD1	cis	parietal	SCAN
rs511415	RIPK4	cis	parietal	SCAN
rs511415	TFF3	cis	cerebellum	SCAN

Chromatin state (count:21 , 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	chr21:40967800-40974000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr21:40969200-40970400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr21:40969200-40970400	Enhancers	Spleen	Spleen
5	chr21:40969200-40970600	Enhancers	Fetal Heart	heart
6	chr21:40969400-40970400	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr21:40969600-40970400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr21:40969800-40970400	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr21:40970000-40970400	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr21:40970000-40970400	Enhancers	Fetal Thymus	thymus
11	chr21:40970000-40970600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr21:40970000-40972400	Weak transcription	Brain Hippocampus Middle	brain
13	chr21:40970000-40973200	Weak transcription	Brain Substantia Nigra	brain
14	chr21:40970200-40970400	Enhancers	Pancreas	Pancrea
15	chr21:40970200-40971200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr21:40970200-40972600	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr21:40970200-40973000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr21:40970200-40973400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr21:40970200-40973600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr21:40970200-40976600	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr21:40970200-40982400	Weak transcription	Rectal Mucosa Donor 31	rectum

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