Variant report

Variant	rs9981573
Chromosome Location	chr21:46116432-46116433
allele	A/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	RAD21	chr21:46116427-46116948	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:46108900..46110482-chr21:46114979..46116763,2	MCF-7	breast:

Variant related genes	Relation type
KRTAP10-12	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11909180	0.96[ASN][1000 genomes]
rs12483730	1.00[JPT][hapmap]
rs2243667	0.88[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2838630	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2838639	0.88[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2838645	0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2838649	0.86[CEU][hapmap];0.88[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2838654	1.00[JPT][hapmap]
rs28797484	0.94[ASN][1000 genomes]
rs4818956	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs56829302	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60154040	0.89[ASN][1000 genomes]
rs60327918	0.91[ASN][1000 genomes]
rs60681728	0.96[ASN][1000 genomes]
rs7283084	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs8132905	0.94[ASN][1000 genomes]
rs8133996	1.00[JPT][hapmap]
rs9637188	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9975249	0.88[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9978932	1.00[JPT][hapmap]
rs9980087	0.88[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9981523	0.82[CHB][hapmap];0.94[ASN][1000 genomes]
rs9981618	0.91[ASN][1000 genomes]
rs9982002	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9984476	0.91[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	nsv916258	chr21:45995986-46624705	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
2	nsv913956	chr21:46096964-46279505	Enhancers Bivalent Enhancer Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	nsv1062245	chr21:46096964-46332587	Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription 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	51 gene(s)	inside rSNPs	diseases
4	nsv544478	chr21:46096964-46332587	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9981573	PWP2	cis	cerebellum	SCAN
rs9981573	PWP2	cis	parietal	SCAN
rs9981573	C21orf67	cis	cerebellum	SCAN
rs9981573	COL18A1	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46101000-46122200	Weak transcription	Right Atrium	heart
2	chr21:46114400-46124400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr21:46114800-46116600	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr21:46115000-46116600	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr21:46115200-46117200	Enhancers	HepG2	liver
6	chr21:46115400-46116600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr21:46115600-46116800	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr21:46115600-46116800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr21:46115600-46117600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr21:46115800-46116600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr21:46115800-46116600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr21:46115800-46117600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr21:46115800-46117800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr21:46116000-46116800	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr21:46116200-46118600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr21:46116400-46117000	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr21:46116400-46120400	Enhancers	H1 Cell Line	embryonic stem cell
18	chr21:46116400-46121800	Weak transcription	H9 Cell Line	embryonic stem cell

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