Variant report

Variant	rs13056281
Chromosome Location	chr22:27571639-27571640
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs13058659	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17348935	0.98[ASN][1000 genomes]
rs17349101	0.98[ASN][1000 genomes]
rs17349346	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs36039022	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56252685	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs713842	1.00[CHB][hapmap]
rs714000	1.00[CHB][hapmap]
rs9613396	0.80[CHB][hapmap];1.00[JPT][hapmap]
rs9625172	1.00[CHB][hapmap]
rs975077	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917333	chr22:26931825-27692024	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	142 gene(s)	inside rSNPs	diseases
2	esv34168	chr22:27289097-27678031	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	esv3413125	chr22:27404463-28121577	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	nsv459860	chr22:27527005-28181436	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv588872	chr22:27527005-28181436	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv459861	chr22:27549141-27575542	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv588873	chr22:27549141-27575542	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	esv2762118	chr22:27549920-27579317	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv459863	chr22:27550764-27575542	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv588874	chr22:27550764-27575542	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv1063215	chr22:27557040-27581253	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13056281	CKAP2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:27567200-27572600	Weak transcription	Ovary	ovary
2	chr22:27569800-27573200	Enhancers	Fetal Brain Female	brain
3	chr22:27570400-27571800	Enhancers	H1 Cell Line	embryonic stem cell
4	chr22:27570400-27571800	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr22:27570400-27572600	Enhancers	Fetal Brain Male	brain
6	chr22:27570600-27571800	Flanking Active TSS	Brain Germinal Matrix	brain
7	chr22:27570600-27572400	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr22:27570600-27572400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr22:27570600-27572600	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
10	chr22:27570800-27571800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr22:27570800-27571800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr22:27570800-27572600	Enhancers	H9 Cell Line	embryonic stem cell
13	chr22:27570800-27574000	Weak transcription	Spleen	Spleen
14	chr22:27571000-27572200	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr22:27571000-27579600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr22:27571400-27571800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr22:27571400-27571800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr22:27571400-27572000	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr22:27571600-27571800	Enhancers	HUVEC	blood vessel
20	chr22:27571600-27571800	Enhancers	NHEK	skin
21	chr22:27571600-27572400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr22:27571600-27572600	Enhancers	iPS-18 Cell Line	embryonic stem cell
23	chr22:27571600-27572600	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr22:27571600-27572800	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr22:27571600-27575600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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