Variant report

Variant	rs61957256
Chromosome Location	chr13:52766599-52766600
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1122934	1.00[ASN][1000 genomes]
rs4091568	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4941729	1.00[ASN][1000 genomes]
rs55667430	0.87[ASN][1000 genomes]
rs55715265	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57345934	1.00[ASN][1000 genomes]
rs61957231	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61957232	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61957233	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61957238	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61957248	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61957249	1.00[ASN][1000 genomes]
rs61957252	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61957253	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61957254	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61957255	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61957258	1.00[ASN][1000 genomes]
rs61957297	1.00[ASN][1000 genomes]
rs61957307	0.87[EUR][1000 genomes]
rs61958782	1.00[ASN][1000 genomes]
rs61958784	1.00[ASN][1000 genomes]
rs61958786	1.00[ASN][1000 genomes]
rs61958788	1.00[ASN][1000 genomes]
rs61958800	1.00[ASN][1000 genomes]
rs61958801	1.00[ASN][1000 genomes]
rs61958802	1.00[ASN][1000 genomes]
rs61958803	1.00[ASN][1000 genomes]
rs61958806	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61958807	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61958860	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61958863	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61958865	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs719349	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7333070	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73502305	1.00[ASN][1000 genomes]
rs73502307	1.00[ASN][1000 genomes]
rs9526818	1.00[ASN][1000 genomes]
rs9526840	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535814	1.00[ASN][1000 genomes]
rs9535818	1.00[ASN][1000 genomes]
rs9535831	1.00[ASN][1000 genomes]
rs9535838	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535839	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535850	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535852	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9535859	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535869	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535870	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535875	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535881	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535886	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535890	1.00[ASN][1000 genomes]
rs9535892	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535893	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9535894	1.00[ASN][1000 genomes]
rs9535897	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535900	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535901	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535902	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535903	1.00[ASN][1000 genomes]
rs9535906	1.00[ASN][1000 genomes]
rs9535909	1.00[ASN][1000 genomes]
rs9535910	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535911	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535913	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9536044	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530718	chr13:52291802-52832752	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS 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	38 gene(s)	inside rSNPs	diseases
2	nsv934070	chr13:52362588-53174923	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv1040931	chr13:52564792-53350914	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv541773	chr13:52564792-53350914	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
5	nsv1037567	chr13:52643647-52802799	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv428288	chr13:52728370-53068132	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
7	nsv976116	chr13:52741751-52768674	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs61957256	CKAP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52734400-52768000	Weak transcription	Aorta	Aorta
2	chr13:52736400-52767200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr13:52737200-52767400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr13:52738400-52767400	Weak transcription	HMEC	breast
5	chr13:52740000-52767200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr13:52741000-52767800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr13:52743400-52767600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr13:52743400-52767800	Weak transcription	Esophagus	oesophagus
9	chr13:52743400-52768200	Weak transcription	Small Intestine	intestine
10	chr13:52745600-52767400	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr13:52747400-52767200	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr13:52752600-52767200	Weak transcription	Psoas Muscle	Psoas
13	chr13:52754400-52767200	Weak transcription	Colonic Mucosa	Colon
14	chr13:52754400-52767800	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr13:52754600-52767000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr13:52754600-52767200	Weak transcription	Fetal Kidney	kidney
17	chr13:52754600-52767200	Weak transcription	NHEK	skin
18	chr13:52754600-52767400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr13:52754600-52767400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr13:52754600-52767400	Weak transcription	Right Ventricle	heart
21	chr13:52754600-52767400	Weak transcription	NHDF-Ad	bronchial
22	chr13:52754600-52767800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr13:52754600-52767800	Weak transcription	Lung	lung
24	chr13:52755600-52767400	Weak transcription	HUVEC	blood vessel
25	chr13:52758000-52768000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr13:52758600-52767000	Weak transcription	Primary B cells from cord blood	blood
27	chr13:52758600-52767400	Weak transcription	A549	lung
28	chr13:52758600-52767600	Weak transcription	Placenta	Placenta
29	chr13:52758600-52767800	Weak transcription	Spleen	Spleen
30	chr13:52758800-52767000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr13:52759000-52767200	Weak transcription	Colon Smooth Muscle	Colon
32	chr13:52759000-52767400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr13:52759200-52767800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr13:52759200-52767800	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr13:52759600-52767400	Weak transcription	Primary B cells from peripheral blood	blood
36	chr13:52760200-52766800	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr13:52760200-52767200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr13:52760200-52767400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr13:52760200-52767400	Weak transcription	Fetal Stomach	stomach
40	chr13:52760200-52767400	Weak transcription	Thymus	Thymus
41	chr13:52760400-52767000	Weak transcription	Duodenum Mucosa	Duodenum
42	chr13:52760400-52767200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr13:52760400-52767400	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr13:52760400-52767400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr13:52760400-52767400	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr13:52760400-52767400	Weak transcription	Stomach Smooth Muscle	stomach
47	chr13:52760400-52767800	Weak transcription	Gastric	stomach
48	chr13:52760400-52767800	Weak transcription	Ovary	ovary
49	chr13:52760400-52768000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr13:52761600-52767400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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