Variant report

Variant	rs550569
Chromosome Location	chr21:40981775-40981776
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	chr21:40980416..40982821-chr21:40984581..40986944,3	MCF-7	breast:
2	chr21:40979099..40981850-chr21:40982315..40985666,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000184809	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs474656	0.91[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs512384	0.90[CHB][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs651029	0.84[JPT][hapmap]
rs671324	0.85[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]

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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs550569	C21orf88	cis	Thyroid	GTEx

Chromatin state (count:23 , 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	chr21:40970400-40981800	Weak transcription	Pancreas	Pancrea
3	chr21:40970800-40984600	Weak transcription	Right Atrium	heart
4	chr21:40973400-40982400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr21:40974000-40982200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr21:40974400-40982200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr21:40974400-40982400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr21:40974400-40982600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr21:40976800-40983200	Weak transcription	Brain Anterior Caudate	brain
10	chr21:40977400-40982200	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr21:40978200-40982000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr21:40980600-40982200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr21:40980800-40982400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr21:40981000-40981800	Strong transcription	H9 Cell Line	embryonic stem cell
15	chr21:40981000-40982000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr21:40981000-40982000	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr21:40981000-40983600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr21:40981400-40981800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr21:40981400-40982600	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr21:40981400-40982800	Enhancers	Duodenum Mucosa	Duodenum
21	chr21:40981400-40983200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr21:40981600-40982600	Enhancers	H1 Cell Line	embryonic stem cell
23	chr21:40981600-40984200	Enhancers	Stomach Mucosa	stomach

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