Variant report

Variant	rs9975249
Chromosome Location	chr21:46107283-46107284
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11909180	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12483730	1.00[JPT][hapmap]
rs2243667	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838630	0.86[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2838639	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838645	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2838649	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2838654	1.00[JPT][hapmap]
rs28797484	0.98[ASN][1000 genomes]
rs4818956	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4818962	0.83[ASN][1000 genomes]
rs56829302	0.94[ASN][1000 genomes]
rs60154040	0.93[ASN][1000 genomes]
rs60327918	0.96[ASN][1000 genomes]
rs60681728	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7283084	0.86[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7283406	0.86[CHB][hapmap]
rs8132905	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8133996	1.00[JPT][hapmap]
rs9637188	0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9978932	1.00[JPT][hapmap]
rs9980087	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9981523	0.82[CHB][hapmap];0.98[ASN][1000 genomes]
rs9981573	0.88[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9981618	0.96[ASN][1000 genomes]
rs9982002	1.00[ASN][1000 genomes]
rs9984476	0.96[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9975249	C21orf67	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46101000-46122200	Weak transcription	Right Atrium	heart
2	chr21:46105600-46107800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr21:46105600-46108200	Enhancers	iPS-18 Cell Line	embryonic stem cell
4	chr21:46105800-46107400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr21:46105800-46107400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr21:46105800-46107600	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr21:46106000-46107400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr21:46106000-46107800	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr21:46106000-46109000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr21:46106200-46107800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr21:46106200-46108000	Enhancers	H1 Cell Line	embryonic stem cell
12	chr21:46106400-46107600	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr21:46106400-46107800	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr21:46106400-46108200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr21:46106600-46107800	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr21:46106600-46107800	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr21:46106800-46107800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr21:46106800-46107800	Enhancers	Fetal Thymus	thymus
19	chr21:46106800-46108400	Bivalent Enhancer	Fetal Muscle Leg	muscle
20	chr21:46106800-46108600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
21	chr21:46107000-46107800	Bivalent Enhancer	Placenta	Placenta
22	chr21:46107000-46108200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr21:46107200-46107600	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr21:46107200-46107600	Bivalent Enhancer	HSMMtube	muscle
25	chr21:46107200-46107800	Bivalent Enhancer	HSMM	muscle

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