Variant report

Variant	rs570510
Chromosome Location	chr21:40901431-40901432
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:40901121..40903929-chr21:40907917..40910902,2	K562	blood:
2	chr21:40891069..40892721-chr21:40900987..40902576,2	MCF-7	breast:
3	chr21:40900284..40901980-chr21:41045530..41047230,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SH3BGR-1	chr21:40898286-40901782	NONHSAT082198

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs12627708	1.00[JPT][hapmap]
rs1734930	1.00[JPT][hapmap]
rs2037669	0.97[EUR][1000 genomes]
rs2837083	1.00[JPT][hapmap]
rs503729	1.00[JPT][hapmap]
rs523372	1.00[JPT][hapmap]
rs528499	1.00[JPT][hapmap]
rs529409	1.00[JPT][hapmap]
rs551439	1.00[JPT][hapmap]
rs551680	1.00[JPT][hapmap]
rs555963	1.00[JPT][hapmap]
rs562285	1.00[JPT][hapmap]
rs563259	1.00[JPT][hapmap]
rs564126	1.00[JPT][hapmap]
rs571227	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs573149	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs585092	1.00[JPT][hapmap]
rs589326	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs602107	1.00[JPT][hapmap]
rs606003	1.00[JPT][hapmap]
rs606414	1.00[JPT][hapmap]
rs611958	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs613758	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs626856	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs628995	1.00[JPT][hapmap]
rs636599	1.00[JPT][hapmap]
rs644080	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs659545	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs659892	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs665778	1.00[JPT][hapmap]
rs680033	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs856994	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv1062088	chr21:40838027-40919253	Enhancers Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	esv2756754	chr21:40857523-40966156	Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	esv2758820	chr21:40857523-40966156	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	esv34779	chr21:40884871-40977473	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv433457	chr21:40900348-40964553	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs570510	NCRNA00114	cis	parietal	SCAN
rs570510	RCAN1	cis	parietal	SCAN
rs570510	DOPEY2	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40888200-40907400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr21:40894400-40901600	Enhancers	Pancreas	Pancrea
3	chr21:40895800-40909600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr21:40896000-40903000	Weak transcription	Brain Substantia Nigra	brain
5	chr21:40900000-40903000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr21:40900000-40905600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr21:40900200-40902800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr21:40900200-40903000	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr21:40900400-40901600	Bivalent Enhancer	Placenta	Placenta
10	chr21:40900400-40902600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr21:40900400-40903000	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr21:40900600-40903000	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr21:40901000-40901600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr21:40901000-40901600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr21:40901000-40901800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr21:40901000-40901800	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr21:40901000-40903400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr21:40901200-40902600	Weak transcription	Right Ventricle	heart
19	chr21:40901200-40910200	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr21:40901400-40909200	Weak transcription	Stomach Mucosa	stomach

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