Variant report

Variant	rs512384
Chromosome Location	chr21:40987887-40987888
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:40895232..40897422-chr21:40987219..40990019,2	MCF-7	breast:
2	chr21:40982969..40984570-chr21:40986006..40988233,2	MCF-7	breast:
3	chr21:40976514..40978882-chr21:40987659..40990131,2	MCF-7	breast:
4	chr21:40986802..40989122-chr21:41045623..41048115,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000184809	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs2837101	0.80[YRI][hapmap]
rs474656	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	0.90[CHB][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs602006	0.81[LWK][hapmap];0.84[MKK][hapmap]
rs651029	0.89[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs666085	0.89[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs667432	0.89[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs671324	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap]
rs673361	0.81[AFR][1000 genomes]
rs856995	0.89[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];0.81[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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs512384	C21orf88	cis	Thyroid	GTEx

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40985600-41002400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr21:40985600-41008400	Weak transcription	Pancreas	Pancrea
3	chr21:40986000-40992400	Weak transcription	Fetal Heart	heart
4	chr21:40986000-41004200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr21:40986800-40988000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr21:40986800-40991000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr21:40987000-40988400	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr21:40987000-40988800	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr21:40987000-40989000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr21:40987000-40989400	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr21:40987000-40999000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr21:40987200-40988200	Active TSS	Rectal Mucosa Donor 31	rectum
13	chr21:40987200-40988400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr21:40987200-40989200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr21:40987200-40989600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr21:40987200-40990000	Strong transcription	H1 Cell Line	embryonic stem cell
17	chr21:40987200-40990000	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr21:40987200-40990200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr21:40987400-40989000	Enhancers	Rectal Mucosa Donor 29	rectum
20	chr21:40987400-40990200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr21:40987600-40996200	Weak transcription	Brain Anterior Caudate	brain
22	chr21:40987800-40988200	Enhancers	Pancreatic Islets	Pancreatic Islet
23	chr21:40987800-40989600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr21:40987800-40992400	Weak transcription	Stomach Mucosa	stomach

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