Variant report

Variant	rs565898
Chromosome Location	chr13:96671578-96671579
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 111 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10508027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11616724	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11618108	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11619636	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12428062	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12430152	1.00[JPT][hapmap]
rs1327640	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1330556	0.88[AFR][1000 genomes]
rs1330557	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16951448	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1788062	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1854174	0.80[ASN][1000 genomes]
rs1854758	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs2129006	0.86[EUR][1000 genomes]
rs2170813	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs2257397	0.80[ASN][1000 genomes]
rs2257398	0.80[ASN][1000 genomes]
rs2262077	0.80[ASN][1000 genomes]
rs2849439	0.87[ASN][1000 genomes]
rs3099362	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3099363	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3101570	1.00[JPT][hapmap]
rs4383020	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4409947	1.00[JPT][hapmap]
rs4547219	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs475882	0.80[CEU][hapmap]
rs4773932	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs490753	0.85[ASN][1000 genomes]
rs492247	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs492744	0.80[ASN][1000 genomes]
rs493423	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs495214	0.89[CEU][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs502311	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs504340	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs526381	0.87[ASN][1000 genomes]
rs526702	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs531432	0.87[AMR][1000 genomes]
rs531549	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs534010	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs534429	0.88[CEU][hapmap]
rs537463	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs539293	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs540213	0.88[CEU][hapmap]
rs544815	0.87[ASN][1000 genomes]
rs547858	0.87[ASN][1000 genomes]
rs56077337	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs562879	0.87[ASN][1000 genomes]
rs564075	0.87[ASN][1000 genomes]
rs565297	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs565851	0.88[CEU][hapmap]
rs568170	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs568945	0.85[ASN][1000 genomes]
rs571059	0.85[AMR][1000 genomes]
rs573909	0.80[ASN][1000 genomes]
rs581462	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs602540	0.80[ASN][1000 genomes]
rs626317	0.84[ASN][1000 genomes]
rs627074	0.87[ASN][1000 genomes]
rs639527	0.87[ASN][1000 genomes]
rs645595	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs647811	0.87[ASN][1000 genomes]
rs6492833	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6492834	0.80[ASN][1000 genomes]
rs649322	0.80[ASN][1000 genomes]
rs651812	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs661544	0.97[ASN][1000 genomes]
rs662884	0.89[CEU][hapmap];0.97[ASN][1000 genomes]
rs672988	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs674565	0.89[CEU][hapmap];0.85[AMR][1000 genomes]
rs675144	0.88[CEU][hapmap]
rs680576	0.87[ASN][1000 genomes]
rs684902	0.82[ASN][1000 genomes]
rs686672	0.82[ASN][1000 genomes]
rs688133	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7139605	0.80[ASN][1000 genomes]
rs72636556	0.83[ASN][1000 genomes]
rs72636562	0.81[ASN][1000 genomes]
rs72636570	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72637833	0.86[EUR][1000 genomes]
rs72637836	0.86[EUR][1000 genomes]
rs72637837	0.86[EUR][1000 genomes]
rs72637840	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72638023	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72638024	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72638031	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7318247	0.80[ASN][1000 genomes]
rs7318449	0.80[ASN][1000 genomes]
rs7330650	0.80[ASN][1000 genomes]
rs7331211	1.00[JPT][hapmap]
rs7332078	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[ASN][1000 genomes]
rs7334320	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs7335209	0.83[ASN][1000 genomes]
rs7338171	0.80[ASN][1000 genomes]
rs7339059	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs7999737	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs816109	0.80[ASN][1000 genomes]
rs816122	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs816142	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9516621	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs9525077	0.88[AFR][1000 genomes]
rs9525079	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs9525134	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9525136	0.80[ASN][1000 genomes]
rs9584324	1.00[JPT][hapmap]
rs9590344	0.89[AFR][1000 genomes];0.83[ASN][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	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
2	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
3	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
4	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
5	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
6	nsv869471	chr13:96622327-97223956	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:96613200-96694200	Weak transcription	A549	lung
2	chr13:96622200-96677200	Weak transcription	NH-A	brain
3	chr13:96651000-96671800	Weak transcription	HSMM	muscle
4	chr13:96657800-96677200	Weak transcription	HSMMtube	muscle
5	chr13:96659400-96672600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr13:96660200-96682200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr13:96660400-96678600	Weak transcription	Duodenum Mucosa	Duodenum
8	chr13:96660600-96676600	Weak transcription	Osteobl	bone
9	chr13:96660800-96672600	Weak transcription	Liver	Liver
10	chr13:96660800-96684800	Weak transcription	Psoas Muscle	Psoas
11	chr13:96663200-96685400	Weak transcription	HMEC	breast
12	chr13:96663800-96672600	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr13:96664000-96677200	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr13:96664200-96677600	Weak transcription	NHDF-Ad	bronchial
15	chr13:96664200-96684800	Weak transcription	NHLF	lung
16	chr13:96667200-96672200	Weak transcription	Brain Hippocampus Middle	brain
17	chr13:96668400-96672600	Weak transcription	Brain Substantia Nigra	brain
18	chr13:96668600-96679400	Weak transcription	Fetal Brain Male	brain
19	chr13:96668600-96704400	Weak transcription	Stomach Smooth Muscle	stomach
20	chr13:96668800-96672800	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr13:96668800-96673600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr13:96668800-96685400	Weak transcription	Gastric	stomach
23	chr13:96669000-96683200	Weak transcription	Esophagus	oesophagus
24	chr13:96669000-96685800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr13:96669000-96686200	Weak transcription	NHEK	skin
26	chr13:96669200-96671600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr13:96669200-96672400	Strong transcription	Fetal Stomach	stomach
28	chr13:96669200-96686800	Weak transcription	Right Ventricle	heart
29	chr13:96669200-96694000	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr13:96669400-96672000	Weak transcription	Fetal Muscle Trunk	muscle
31	chr13:96669400-96672200	Weak transcription	GM12878-XiMat	blood
32	chr13:96669400-96672600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr13:96669400-96672600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr13:96669400-96673000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr13:96669400-96676600	Weak transcription	Aorta	Aorta
36	chr13:96669400-96677000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr13:96669400-96677000	Weak transcription	Brain Germinal Matrix	brain
38	chr13:96669400-96677200	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr13:96669400-96677200	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr13:96669400-96680000	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr13:96669400-96685400	Weak transcription	Fetal Kidney	kidney
42	chr13:96669400-96685600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr13:96669400-96685600	Weak transcription	Fetal Brain Female	brain
44	chr13:96669400-96694000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr13:96669400-96704600	Weak transcription	Brain Anterior Caudate	brain
46	chr13:96669600-96672000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr13:96669600-96672000	Weak transcription	Left Ventricle	heart
48	chr13:96669600-96672200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr13:96669600-96674200	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr13:96669600-96677400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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