Variant report

Variant	rs2838768
Chromosome Location	chr21:46491341-46491342
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr21:46490374-46491625	K562	blood:	n/a	n/a
2	POLR2A	chr21:46490960-46491799	Hela-S3	cervix:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:46348854..46378176-chr21:46489799..46500436,75	K562	blood:
2	chr21:46363747..46379047-chr21:46484156..46498795,67	K562	blood:
3	chr21:46355061..46362857-chr21:46490375..46496482,13	K562	blood:
4	chr21:46473237..46476363-chr21:46488566..46491608,3	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C21orf67-11	chr21:46490871-46493126	NONHSAT082913
2	lnc-C21orf67-11	chr21:46490870-46493126	NR_027292

No data

Variant related genes	Relation type
ADARB1	TF binding region
ENSG00000272825	Chromatin interaction
ENSG00000160256	Chromatin interaction
ENSG00000160255	Chromatin interaction
ENSG00000273027	Chromatin interaction
ENSG00000183250	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs2838764	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2838767	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838770	1.00[CEU][hapmap];0.93[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28760601	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8132098	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9977041	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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	nsv834110	chr21:46316183-46505151	Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2838768	C21orf122	cis	multi-tissue	Pritchard

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46475200-46493400	Weak transcription	Right Atrium	heart
2	chr21:46475400-46493200	Weak transcription	Spleen	Spleen
3	chr21:46484600-46493400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr21:46484800-46493200	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr21:46485400-46492800	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr21:46485600-46493600	Weak transcription	Aorta	Aorta
7	chr21:46487600-46493200	Enhancers	Fetal Muscle Trunk	muscle
8	chr21:46487800-46493200	Weak transcription	Fetal Heart	heart
9	chr21:46487800-46493600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr21:46488200-46493400	Weak transcription	Primary T cells from cord blood	blood
11	chr21:46489200-46492600	Enhancers	HSMM	muscle
12	chr21:46489600-46491600	Enhancers	K562	blood
13	chr21:46489600-46492000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr21:46489600-46493400	Enhancers	HSMMtube	muscle
15	chr21:46489800-46491600	Enhancers	Fetal Muscle Leg	muscle
16	chr21:46489800-46492200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr21:46489800-46492400	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr21:46489800-46493200	Weak transcription	Hela-S3	cervix
19	chr21:46489800-46493400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr21:46490200-46492600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr21:46490200-46492800	Weak transcription	Stomach Smooth Muscle	stomach
22	chr21:46490200-46493200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr21:46490200-46493200	Weak transcription	Esophagus	oesophagus
24	chr21:46490200-46493400	Weak transcription	NH-A	brain
25	chr21:46490400-46492400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr21:46490400-46492600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr21:46490400-46492800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr21:46490400-46493200	Weak transcription	HMEC	breast
29	chr21:46490400-46493200	Weak transcription	NHEK	skin
30	chr21:46490400-46493400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr21:46490600-46492600	Weak transcription	Placenta	Placenta
32	chr21:46490600-46493200	Weak transcription	Fetal Intestine Small	intestine
33	chr21:46491000-46492600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr21:46491000-46493200	Enhancers	Muscle Satellite Cultured Cells	--
35	chr21:46491000-46493400	Weak transcription	Brain Substantia Nigra	brain
36	chr21:46491200-46492800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr21:46491200-46493200	Weak transcription	Skeletal Muscle Male	skeletal muscle

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