Variant report

Variant	rs9646007
Chromosome Location	chr13:52985456-52985457
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:52983388..52985716-chr13:52991377..52992928,2	K562	blood:
2	chr13:52978712..52982217-chr13:52984992..52988158,3	K562	blood:
3	chr13:52984347..52986130-chr13:52989381..52990999,2	K562	blood:
4	chr13:52985298..52988100-chr13:53012949..53014836,2	K562	blood:
5	chr13:52979314..52982217-chr13:52984992..52987265,2	K562	blood:

Variant related genes	Relation type
ENSG00000136100	Chromatin interaction
ENSG00000136114	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs41292810	0.85[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	nsv900084	chr13:52835231-53119704	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	esv1838257	chr13:52971893-53231454	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9646007	CKAP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52980200-52985600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr13:52980200-52988400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr13:52980200-52989800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr13:52980200-53002000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr13:52980200-53021600	Weak transcription	Small Intestine	intestine
6	chr13:52980600-52985600	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr13:52980600-52985600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr13:52980600-52985800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr13:52980600-52985800	Weak transcription	Aorta	Aorta
10	chr13:52980600-52985800	Weak transcription	Brain Angular Gyrus	brain
11	chr13:52980600-52985800	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr13:52980600-52986200	Weak transcription	Spleen	Spleen
13	chr13:52980600-52986400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr13:52980600-52986400	Weak transcription	Brain Substantia Nigra	brain
15	chr13:52980600-52986400	Weak transcription	Ovary	ovary
16	chr13:52980600-52986600	Weak transcription	HepG2	liver
17	chr13:52980600-52987000	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr13:52980600-52988200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr13:52980600-52988200	Weak transcription	Esophagus	oesophagus
20	chr13:52980600-52988200	Weak transcription	Fetal Stomach	stomach
21	chr13:52980600-52988200	Weak transcription	Gastric	stomach
22	chr13:52980600-52988200	Weak transcription	Pancreas	Pancrea
23	chr13:52980600-52988400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr13:52980600-52988600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr13:52980600-52989800	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr13:52980800-52985600	Weak transcription	Fetal Muscle Trunk	muscle
27	chr13:52980800-52985600	Weak transcription	NHDF-Ad	bronchial
28	chr13:52980800-52985800	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr13:52980800-52985800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr13:52980800-52985800	Weak transcription	Duodenum Mucosa	Duodenum
31	chr13:52980800-52985800	Weak transcription	Fetal Intestine Large	intestine
32	chr13:52980800-52985800	Weak transcription	Stomach Smooth Muscle	stomach
33	chr13:52980800-52985800	Weak transcription	NH-A	brain
34	chr13:52980800-52986000	Weak transcription	Primary B cells from peripheral blood	blood
35	chr13:52980800-52986200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr13:52980800-52986200	Weak transcription	Fetal Brain Female	brain
37	chr13:52980800-52986200	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr13:52980800-52986400	Weak transcription	Liver	Liver
39	chr13:52980800-52986400	Weak transcription	Placenta	Placenta
40	chr13:52980800-52986400	Weak transcription	Rectal Smooth Muscle	rectum
41	chr13:52980800-52987000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr13:52980800-52987800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr13:52980800-52988200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr13:52980800-52988200	Weak transcription	Brain Anterior Caudate	brain
45	chr13:52980800-52988200	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr13:52980800-52988200	Weak transcription	Colonic Mucosa	Colon
47	chr13:52980800-52988200	Weak transcription	Right Ventricle	heart
48	chr13:52980800-52988200	Weak transcription	GM12878-XiMat	blood
49	chr13:52980800-52988400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr13:52980800-52988400	Weak transcription	Brain Cingulate Gyrus	brain

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