Variant report

Variant	rs9535897
Chromosome Location	chr13:52767910-52767911
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:52701771..52705558-chr13:52767896..52769871,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NEK3-1	chr13:52766939-52768570	NONHSAT033977

Variant related genes	Relation type
ENSG00000197168	Chromatin interaction

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]
rs61957256	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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]
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
rs9535897	CKAP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52734400-52768000	Weak transcription	Aorta	Aorta
2	chr13:52743400-52768200	Weak transcription	Small Intestine	intestine
3	chr13:52758000-52768000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr13:52760400-52768000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr13:52765800-52768200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr13:52766400-52770000	Active TSS	Right Atrium	heart
7	chr13:52767000-52768000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr13:52767000-52768000	Flanking Active TSS	Dnd41	blood
9	chr13:52767200-52768000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
10	chr13:52767200-52768000	Flanking Active TSS	Brain Anterior Caudate	brain
11	chr13:52767200-52768200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
12	chr13:52767200-52768200	Flanking Active TSS	Liver	Liver
13	chr13:52767200-52768400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr13:52767200-52769000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr13:52767200-52769200	Active TSS	H9 Cell Line	embryonic stem cell
16	chr13:52767200-52769200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr13:52767200-52770000	Active TSS	ES-I3 Cell Line	embryonic stem cell
18	chr13:52767200-52770000	Active TSS	Psoas Muscle	Psoas
19	chr13:52767200-52770200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr13:52767400-52768000	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr13:52767400-52768000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
22	chr13:52767400-52768000	Enhancers	Sigmoid Colon	Sigmoid Colon
23	chr13:52767400-52768000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
24	chr13:52767400-52768400	Flanking Active TSS	Adipose Nuclei	Adipose
25	chr13:52767400-52769000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr13:52767400-52769000	Active TSS	iPS-18 Cell Line	embryonic stem cell
27	chr13:52767400-52769200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr13:52767400-52769200	Active TSS	HUES48 Cell Line	embryonic stem cell
29	chr13:52767400-52769200	Active TSS	HUES64 Cell Line	embryonic stem cell
30	chr13:52767400-52769200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr13:52767400-52769400	Active TSS	Right Ventricle	heart
32	chr13:52767400-52769600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr13:52767400-52769600	Active TSS	GM12878-XiMat	blood
34	chr13:52767400-52769800	Active TSS	Muscle Satellite Cultured Cells	--
35	chr13:52767400-52769800	Active TSS	NHDF-Ad	bronchial
36	chr13:52767400-52770000	Active TSS	H1 Cell Line	embryonic stem cell
37	chr13:52767400-52770000	Active TSS	HUES6 Cell Line	embryonic stem cell
38	chr13:52767400-52770000	Active TSS	iPS-15b Cell Line	embryonic stem cell
39	chr13:52767400-52770000	Active TSS	Brain Cingulate Gyrus	brain
40	chr13:52767400-52770000	Active TSS	Colonic Mucosa	Colon
41	chr13:52767400-52770000	Active TSS	Left Ventricle	heart
42	chr13:52767400-52770000	Active TSS	NHLF	lung
43	chr13:52767600-52768000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
44	chr13:52767600-52768000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
45	chr13:52767600-52768000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
46	chr13:52767600-52768000	Flanking Active TSS	HMEC	breast
47	chr13:52767600-52768000	Flanking Active TSS	HUVEC	blood vessel
48	chr13:52767600-52768000	Flanking Active TSS	Osteobl	bone
49	chr13:52767600-52768200	Flanking Active TSS	Primary T cells from cord blood	blood
50	chr13:52767600-52768200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood

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