Variant report

Variant	rs9561988
Chromosome Location	chr13:96581889-96581890
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	chr13:96575800..96578505-chr13:96580994..96583120,2	MCF-7	breast:

Extended variants
information (count: 137 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:130)

rs_ID	r²[population]
rs1015068	0.83[AMR][1000 genomes]
rs11070154	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11070157	0.83[AMR][1000 genomes]
rs1114308	0.83[AMR][1000 genomes]
rs11616658	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11619333	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11619490	0.81[AMR][1000 genomes]
rs11839843	0.82[EUR][1000 genomes]
rs11840966	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11841021	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11842396	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12858210	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12870771	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12876018	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1411557	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1537030	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1537031	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17189895	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17189951	0.82[AMR][1000 genomes]
rs1813179	0.81[AMR][1000 genomes]
rs1872161	0.82[AMR][1000 genomes]
rs2026819	0.83[AMR][1000 genomes]
rs2062276	0.83[AMR][1000 genomes]
rs2129005	0.81[AMR][1000 genomes]
rs2170812	0.81[AMR][1000 genomes]
rs2389532	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2389570	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2389571	0.81[AMR][1000 genomes]
rs28649586	0.83[AMR][1000 genomes]
rs34738594	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34816227	0.81[AMR][1000 genomes]
rs35423192	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35685996	0.81[AMR][1000 genomes]
rs35836619	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35898412	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs36079088	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36101002	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3782989	0.82[AMR][1000 genomes]
rs3825424	0.82[AMR][1000 genomes]
rs4547218	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4771923	0.83[AMR][1000 genomes]
rs4773928	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4773929	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4773933	0.81[AMR][1000 genomes]
rs4773934	0.81[AMR][1000 genomes]
rs4773935	0.80[AMR][1000 genomes]
rs55822301	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56322430	0.82[EUR][1000 genomes]
rs57924129	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59592654	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60677558	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61972920	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6492824	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6492825	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6492827	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67447270	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7317285	0.83[AMR][1000 genomes]
rs7321296	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7322566	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7323150	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7323734	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7323780	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7324957	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7325690	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7325915	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7327532	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7328703	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7331461	0.82[AMR][1000 genomes]
rs7331926	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7332683	0.81[AMR][1000 genomes]
rs7333370	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7333843	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7334100	0.82[AMR][1000 genomes]
rs7335319	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7335514	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7336373	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7336483	0.82[AFR][1000 genomes]
rs7337653	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7338224	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7338859	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs764714	0.81[AMR][1000 genomes]
rs7981923	0.83[EUR][1000 genomes]
rs7982337	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7983546	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7984584	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7986005	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7992875	0.81[AMR][1000 genomes]
rs7998353	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs8000849	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8002064	0.84[EUR][1000 genomes]
rs9556502	0.83[EUR][1000 genomes]
rs9556503	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9556504	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9556505	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9556506	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9556508	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9556509	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9556511	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9556512	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9556513	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9556515	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9556518	0.83[AMR][1000 genomes]
rs9556520	0.83[AMR][1000 genomes]
rs9556523	0.81[AMR][1000 genomes]
rs9561964	0.83[EUR][1000 genomes]
rs9561967	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9561969	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9561971	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9561973	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9561974	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9561975	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9561976	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9561981	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9561984	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9561985	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9561987	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9561991	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9561995	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9561996	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9561998	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9562003	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9562005	0.89[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs9562006	0.95[ASN][1000 genomes]
rs9562007	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9562008	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9562012	0.83[AMR][1000 genomes]
rs9562015	0.83[AMR][1000 genomes]
rs9562016	0.83[AMR][1000 genomes]
rs9562018	0.81[AMR][1000 genomes]
rs9670470	0.82[EUR][1000 genomes];0.94[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	nsv832691	chr13:96478098-96659823	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv900935	chr13:96497070-96631221	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1050430	chr13:96508530-97020734	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv541883	chr13:96508530-97020734	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv1041165	chr13:96522021-96966520	Enhancers Bivalent/Poised TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv1051574	chr13:96550653-96779248	Strong transcription Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv1040320	chr13:96573646-96790859	Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9561988	DNAJC3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:96495000-96590800	Weak transcription	Rectal Smooth Muscle	rectum
2	chr13:96536200-96587200	Weak transcription	Stomach Smooth Muscle	stomach
3	chr13:96543000-96586800	Weak transcription	Brain Hippocampus Middle	brain
4	chr13:96549400-96586400	Weak transcription	Hela-S3	cervix
5	chr13:96558400-96586600	Weak transcription	Right Ventricle	heart
6	chr13:96559600-96583000	Weak transcription	Pancreas	Pancrea
7	chr13:96559600-96586400	Weak transcription	A549	lung
8	chr13:96559800-96583400	Weak transcription	Esophagus	oesophagus
9	chr13:96559800-96588600	Weak transcription	Gastric	stomach
10	chr13:96566800-96587000	Weak transcription	Colon Smooth Muscle	Colon
11	chr13:96568600-96582000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr13:96568600-96582800	Weak transcription	Left Ventricle	heart
13	chr13:96568600-96583000	Weak transcription	Ovary	ovary
14	chr13:96571000-96588600	Weak transcription	Psoas Muscle	Psoas
15	chr13:96577000-96623200	Weak transcription	NHLF	lung
16	chr13:96577200-96582000	Weak transcription	HSMMtube	muscle
17	chr13:96577200-96582800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr13:96577200-96583000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr13:96577200-96585600	Weak transcription	NHDF-Ad	bronchial
20	chr13:96577200-96587600	Weak transcription	HepG2	liver
21	chr13:96577200-96598000	Weak transcription	HMEC	breast
22	chr13:96577600-96582000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr13:96577800-96608800	Weak transcription	NHEK	skin
24	chr13:96579000-96587200	Weak transcription	NH-A	brain
25	chr13:96579000-96587600	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr13:96580600-96582000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr13:96580600-96582000	ZNF genes & repeats	Fetal Intestine Large	intestine
28	chr13:96580600-96585000	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
29	chr13:96580600-96585400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
30	chr13:96580800-96582200	ZNF genes & repeats	Adipose Nuclei	Adipose
31	chr13:96580800-96583400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr13:96580800-96583800	ZNF genes & repeats	Fetal Muscle Leg	muscle
33	chr13:96580800-96585600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
34	chr13:96580800-96588600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr13:96581000-96582400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr13:96581000-96582400	ZNF genes & repeats	Brain Germinal Matrix	brain
37	chr13:96581000-96583600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
38	chr13:96581400-96582800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr13:96581400-96583600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr13:96581400-96584200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr13:96581600-96582000	ZNF genes & repeats	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr13:96581600-96582000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr13:96581600-96582000	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
44	chr13:96581600-96582000	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr13:96581600-96582000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
46	chr13:96581600-96582400	ZNF genes & repeats	Fetal Brain Male	brain
47	chr13:96581600-96582400	ZNF genes & repeats	Fetal Kidney	kidney
48	chr13:96581600-96582400	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
49	chr13:96581600-96583000	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
50	chr13:96581600-96583200	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links