Variant report

Variant	rs599163
Chromosome Location	chr21:40972798-40972799
allele	A/C/T
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	POLR2A	chr21:40972572-40972865	H1-neurons	neurons:	n/a	n/a
2	POLR2A	chr21:40972463-40972815	H1-neurons	neurons:	n/a	n/a

Variant related genes	Relation type
C21orf88	TF binding region

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs535457	0.84[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs536444	0.84[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs583953	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60292849	0.83[EUR][1000 genomes]
rs661650	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs663956	1.00[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	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
4	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
5	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40965600-40976400	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr21:40967800-40974000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr21:40970000-40973200	Weak transcription	Brain Substantia Nigra	brain
4	chr21:40970200-40973000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr21:40970200-40973400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr21:40970200-40973600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr21:40970200-40976600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr21:40970200-40982400	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr21:40970400-40972800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr21:40970400-40976800	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr21:40970400-40979800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr21:40970400-40981800	Weak transcription	Pancreas	Pancrea
13	chr21:40970600-40973200	Weak transcription	Fetal Heart	heart
14	chr21:40970600-40973400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr21:40970800-40984600	Weak transcription	Right Atrium	heart
16	chr21:40971800-40973200	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr21:40971800-40973400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr21:40972400-40974000	Enhancers	Brain Hippocampus Middle	brain
19	chr21:40972600-40974200	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr21:40972600-40974400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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