Variant report

Variant	rs2838649
Chromosome Location	chr21:46120500-46120501
allele	C/T
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	HEY1	chr21:46120484-46121068	HepG2	liver:	n/a	n/a
2	MYBL2	chr21:46120450-46120997	HepG2	liver:	n/a	n/a
3	MAX	chr21:46120449-46121073	HepG2	liver:	n/a	n/a
4	MAX	chr21:46120412-46121096	HepG2	liver:	n/a	n/a
5	EP300	chr21:46120499-46121050	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
KRTAP10-13P	TF binding region

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11909180	0.96[ASN][1000 genomes]
rs12483730	1.00[JPT][hapmap]
rs2243667	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2838615	0.85[CHD][hapmap]
rs2838616	0.85[CHD][hapmap]
rs2838630	0.86[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2838639	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2838645	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2838654	1.00[JPT][hapmap]
rs28797484	0.94[ASN][1000 genomes]
rs4818956	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs56829302	0.90[ASN][1000 genomes]
rs60154040	0.89[ASN][1000 genomes]
rs60327918	0.91[ASN][1000 genomes]
rs60681728	0.96[ASN][1000 genomes]
rs7283084	0.86[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7283406	0.86[CHB][hapmap]
rs8132905	0.94[ASN][1000 genomes]
rs8133996	1.00[JPT][hapmap]
rs9637188	0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9975249	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9978932	1.00[JPT][hapmap]
rs9980087	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9981523	0.82[CHB][hapmap];0.94[ASN][1000 genomes]
rs9981573	0.86[CEU][hapmap];0.88[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9981618	0.91[ASN][1000 genomes]
rs9982002	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2838649	NCRNA00175	cis	parietal	SCAN
rs2838649	C21orf67	cis	cerebellum	SCAN

Chromatin state (count:19 , 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	chr21:46116400-46121800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr21:46116600-46121000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr21:46118200-46120600	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr21:46118400-46121600	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr21:46118400-46123200	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr21:46118400-46123400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr21:46118600-46121800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr21:46118600-46121800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr21:46118800-46120800	Enhancers	HepG2	liver
12	chr21:46119600-46120600	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr21:46119600-46120800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr21:46119800-46120600	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr21:46119800-46122400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr21:46120200-46121800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr21:46120400-46121600	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr21:46120400-46121800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr21:46120400-46121800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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