Variant report

Variant	rs474656
Chromosome Location	chr21:40986120-40986121
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	GATA3	chr21:40985350-40986224	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr21:40982969..40984570-chr21:40986006..40988233,2	MCF-7	breast:
2	chr21:40985808..40987789-chr21:41000169..41002424,2	MCF-7	breast:
3	chr21:40950925..40952824-chr21:40985213..40987161,2	MCF-7	breast:

Variant related genes	Relation type
C21orf88	TF binding region
ENSG00000184809	Chromatin interaction
ENSG00000225330	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs512384	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs550569	0.91[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs602006	0.83[YRI][hapmap]
rs651029	0.88[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs666085	0.89[CEU][hapmap];0.82[CHB][hapmap];0.80[JPT][hapmap]
rs667432	0.88[CEU][hapmap];0.82[CHB][hapmap];0.84[JPT][hapmap]
rs671324	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap]
rs856995	0.89[CEU][hapmap];0.82[CHB][hapmap];0.80[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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
5	esv11702	chr21:40981640-40987483	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv587484	chr21:40983133-40986120	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs474656	C21orf88	cis	Thyroid	GTEx

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40982800-40986400	Active TSS	H9 Cell Line	embryonic stem cell
2	chr21:40983200-40987600	Active TSS	Brain Anterior Caudate	brain
3	chr21:40983400-40986200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr21:40983600-40986200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr21:40983600-40986600	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
6	chr21:40984000-40986200	Active TSS	H1 Cell Line	embryonic stem cell
7	chr21:40984200-40987400	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr21:40984400-40986400	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr21:40985200-40986200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr21:40985600-40986200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr21:40985600-40986200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
12	chr21:40985600-40986800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr21:40985600-40986800	Weak transcription	Right Atrium	heart
14	chr21:40985600-41002400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr21:40985600-41008400	Weak transcription	Pancreas	Pancrea
16	chr21:40985800-40986200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr21:40985800-40986200	Bivalent Enhancer	Brain Germinal Matrix	brain
18	chr21:40985800-40986200	Bivalent Enhancer	Fetal Kidney	kidney
19	chr21:40985800-40986200	Enhancers	NH-A	brain
20	chr21:40985800-40986400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr21:40985800-40986600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
22	chr21:40985800-40987000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
23	chr21:40985800-40987000	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr21:40986000-40986200	Active TSS	iPS-20b Cell Line	embryonic stem cell
25	chr21:40986000-40986200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr21:40986000-40986400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr21:40986000-40986600	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
28	chr21:40986000-40986600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr21:40986000-40986600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
30	chr21:40986000-40986600	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr21:40986000-40987200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr21:40986000-40992400	Weak transcription	Fetal Heart	heart
33	chr21:40986000-41004200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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