Variant report

Variant	rs2001630
Chromosome Location	chr21:46473160-46473161
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:46425396..46428142-chr21:46471479..46473629,2	MCF-7	breast:
2	chr21:46411537..46413701-chr21:46472011..46474537,2	MCF-7	breast:
3	chr21:46461656..46464324-chr21:46472065..46476080,4	K562	blood:
4	chr21:46472629..46476505-chr21:46493480..46496776,4	K562	blood:
5	chr21:46471253..46475067-chr21:46492692..46495529,4	MCF-7	breast:
6	chr21:46465969..46468052-chr21:46471400..46473443,2	MCF-7	breast:
7	chr21:46364819..46367471-chr21:46472297..46474771,2	K562	blood:
8	chr21:46471533..46473565-chr21:46485683..46487648,2	MCF-7	breast:
9	chr21:46467385..46475999-chr21:46491097..46497836,11	MCF-7	breast:
10	chr21:46451651..46453473-chr21:46473060..46475568,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000268856	Chromatin interaction
ENSG00000197381	Chromatin interaction
ENSG00000235374	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12482061	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12627022	0.83[ASN][1000 genomes]
rs12627119	0.81[ASN][1000 genomes]
rs2838755	0.83[ASN][1000 genomes]
rs4818757	0.84[ASN][1000 genomes]
rs58681776	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73230629	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73230630	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73230637	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8131782	0.81[ASN][1000 genomes]
rs869957	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs869958	0.94[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.94[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	nsv913970	chr21:46305175-46487831	Bivalent Enhancer Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv913976	chr21:46306161-46487831	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2001630	KRTAP10-10	cis	cerebellum	SCAN
rs2001630	KRTAP10-2	cis	parietal	SCAN
rs2001630	SIK1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46455200-46474800	Weak transcription	Right Atrium	heart
2	chr21:46465600-46474800	Weak transcription	Aorta	Aorta
3	chr21:46468800-46474800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr21:46469000-46474600	Enhancers	Fetal Muscle Leg	muscle
5	chr21:46469600-46473200	Flanking Active TSS	Hela-S3	cervix
6	chr21:46469600-46473400	Enhancers	Fetal Muscle Trunk	muscle
7	chr21:46470600-46474800	Weak transcription	Right Ventricle	heart
8	chr21:46471600-46484200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr21:46471800-46473400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr21:46471800-46473800	Enhancers	Muscle Satellite Cultured Cells	--
11	chr21:46471800-46474000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr21:46471800-46474000	Enhancers	HSMM	muscle
13	chr21:46471800-46474800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr21:46471800-46474800	Weak transcription	Gastric	stomach
15	chr21:46471800-46474800	Weak transcription	Pancreas	Pancrea
16	chr21:46471800-46474800	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr21:46471800-46475800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr21:46471800-46478000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr21:46471800-46480200	Weak transcription	Lung	lung
20	chr21:46472200-46473600	Weak transcription	HSMMtube	muscle
21	chr21:46472200-46475800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr21:46472800-46473200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
23	chr21:46473000-46473200	Enhancers	H1 Cell Line	embryonic stem cell
24	chr21:46473000-46473800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr21:46473000-46474200	Enhancers	Fetal Lung	lung

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