Variant report

Variant	rs9535828
Chromosome Location	chr13:52573422-52573423
allele	A/G
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	chr13:52564916..52570042-chr13:52571727..52575592,5	MCF-7	breast:
2	chr13:52571069..52573595-chr13:52575661..52577767,2	K562	blood:
3	chr13:52494195..52496775-chr13:52571479..52573811,2	MCF-7	breast:
4	chr13:52572621..52575296-chr13:52579187..52581060,2	K562	blood:
5	chr13:52566849..52570695-chr13:52572398..52574312,4	K562	blood:
6	chr13:52568982..52573456-chr13:52591589..52596221,4	K562	blood:
7	chr13:52573284..52575867-chr13:52579600..52581887,2	K562	blood:
8	chr13:52565945..52573624-chr13:52584322..52588378,8	K562	blood:
9	chr13:52571352..52573505-chr13:52585420..52587212,2	MCF-7	breast:
10	chr13:52550522..52553056-chr13:52572837..52575567,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000253710	Chromatin interaction
ENSG00000123191	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs11616964	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11620583	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12584961	0.80[EUR][1000 genomes]
rs1801243	0.89[CEU][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1801244	0.85[CEU][hapmap];0.87[MEX][hapmap];0.87[AMR][1000 genomes]
rs1886542	0.87[CHD][hapmap];0.83[MEX][hapmap];0.89[YRI][hapmap]
rs1886547	0.96[CEU][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.90[YRI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1924611	1.00[CEU][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1951922	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1998696	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2004866	0.86[ASW][hapmap];1.00[CEU][hapmap];0.87[CHD][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2181891	0.89[CEU][hapmap];0.96[MEX][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2274202	0.87[CHD][hapmap];0.83[MEX][hapmap]
rs2296348	0.87[CHD][hapmap]
rs2296349	0.87[CHD][hapmap];0.83[MEX][hapmap]
rs2408544	1.00[CEU][hapmap];0.90[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2408549	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2408550	0.96[CEU][hapmap];0.84[CHD][hapmap];0.80[GIH][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2408551	0.93[CEU][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.82[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2408609	0.86[CHD][hapmap];0.83[MEX][hapmap]
rs2408611	0.82[CHD][hapmap]
rs2897977	0.87[CHD][hapmap]
rs3368	0.89[YRI][hapmap]
rs35895576	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3742288	0.85[CEU][hapmap];0.83[MEX][hapmap];0.87[AMR][1000 genomes]
rs3825527	0.85[CEU][hapmap];0.88[MEX][hapmap];0.87[AMR][1000 genomes]
rs3825528	0.86[ASW][hapmap];1.00[CEU][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4297592	0.96[CEU][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55772266	0.81[EUR][1000 genomes]
rs61958812	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6650383	0.80[AMR][1000 genomes]
rs723102	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs723103	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7327634	0.86[ASW][hapmap];1.00[CEU][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7337430	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs747781	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs750290	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs755363	0.96[CEU][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs7991237	0.96[CEU][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap]
rs7993492	0.86[ASN][1000 genomes]
rs7994928	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7995946	0.96[CEU][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs7999812	0.84[CEU][hapmap];0.87[AMR][1000 genomes]
rs9316563	1.00[CEU][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9526819	0.87[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9526821	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9526832	0.83[EUR][1000 genomes]
rs9526837	0.96[CEU][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap]
rs9526842	0.87[YRI][hapmap]
rs9535812	0.89[CEU][hapmap];1.00[MEX][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9535817	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9535819	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9535822	0.87[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9535823	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9535826	0.87[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9535829	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9535830	0.84[ASN][1000 genomes]
rs9535832	0.82[CEU][hapmap];0.83[CHD][hapmap];0.86[ASN][1000 genomes]
rs9535833	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535836	1.00[CEU][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.90[YRI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9535851	0.96[CEU][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9535856	0.92[CEU][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap]
rs9535858	0.96[CEU][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];0.89[TSI][hapmap];0.90[YRI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9535860	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9535862	0.96[CEU][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9535866	0.96[CEU][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs9535878	0.87[CHD][hapmap];0.83[MEX][hapmap];0.89[YRI][hapmap]
rs9535880	0.87[CHD][hapmap]
rs9535882	0.89[YRI][hapmap]
rs9535887	0.87[CHD][hapmap];0.83[MEX][hapmap];0.89[YRI][hapmap]
rs9563084	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9563089	1.00[CEU][hapmap];0.87[CHD][hapmap];0.80[GIH][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.90[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9568681	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9568684	0.84[JPT][hapmap]
rs9568693	0.83[EUR][1000 genomes]
rs9568695	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9568713	0.96[CEU][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];0.90[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv1044310	chr13:52321564-52643924	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv1050117	chr13:52325116-52643924	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	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
5	nsv1041996	chr13:52544805-52581501	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	n/a
6	esv2763022	chr13:52544978-52581513	Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	n/a
7	nsv900082	chr13:52555288-52709938	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
8	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
9	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9535828	CKAP2	cis	parietal	SCAN
rs9535828	NEK3	cis	cerebellum	SCAN
rs9535828	NEK3	Cis_1M	lymphoblastoid	RTeQTL
rs9535828	NCRNA00282	cis	cerebellum	SCAN
rs9535828	CKAP2	cis	cerebellum	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52569200-52575600	Enhancers	Stomach Mucosa	stomach
2	chr13:52569400-52574400	Enhancers	Placenta	Placenta
3	chr13:52569400-52574600	Enhancers	Fetal Heart	heart
4	chr13:52569400-52575000	Enhancers	Fetal Muscle Leg	muscle
5	chr13:52569400-52575800	Enhancers	Fetal Intestine Large	intestine
6	chr13:52570000-52575000	Enhancers	Duodenum Mucosa	Duodenum
7	chr13:52570400-52573600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr13:52570600-52574000	Weak transcription	Brain Cingulate Gyrus	brain
9	chr13:52570600-52575400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr13:52570800-52573800	Weak transcription	Brain Anterior Caudate	brain
11	chr13:52570800-52577600	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr13:52570800-52585000	Weak transcription	Colonic Mucosa	Colon
13	chr13:52570800-52585200	Weak transcription	Aorta	Aorta
14	chr13:52571000-52573800	Weak transcription	Lung	lung
15	chr13:52571000-52574200	Weak transcription	Fetal Brain Female	brain
16	chr13:52571000-52583800	Weak transcription	Brain Germinal Matrix	brain
17	chr13:52571400-52574000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr13:52571600-52573800	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr13:52571800-52573800	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr13:52571800-52573800	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr13:52571800-52573800	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr13:52571800-52574000	Enhancers	H9 Cell Line	embryonic stem cell
23	chr13:52572000-52574000	Enhancers	H1 Cell Line	embryonic stem cell
24	chr13:52572000-52575800	Enhancers	Fetal Intestine Small	intestine
25	chr13:52572200-52573600	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr13:52572200-52573600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr13:52572200-52573600	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr13:52572200-52573800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr13:52572200-52574200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr13:52572200-52574400	Enhancers	Fetal Muscle Trunk	muscle
31	chr13:52572200-52574400	Enhancers	Placenta Amnion	Placenta Amnion
32	chr13:52572200-52575200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr13:52572600-52573600	Flanking Active TSS	HepG2	liver
34	chr13:52572600-52574200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr13:52572800-52573600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr13:52572800-52573600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr13:52572800-52573600	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr13:52572800-52573800	Enhancers	Pancreas	Pancrea
39	chr13:52572800-52574200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr13:52572800-52574600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr13:52573000-52573600	Enhancers	Brain Angular Gyrus	brain
42	chr13:52573000-52573600	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr13:52573000-52573800	Flanking Active TSS	K562	blood
44	chr13:52573000-52574000	Enhancers	Fetal Thymus	thymus
45	chr13:52573000-52574200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr13:52573000-52574200	Enhancers	Right Ventricle	heart
47	chr13:52573000-52574400	Enhancers	Psoas Muscle	Psoas
48	chr13:52573200-52573600	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr13:52573200-52573800	Enhancers	Adipose Nuclei	Adipose
50	chr13:52573200-52573800	Weak transcription	Right Atrium	heart

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