Variant report

Variant	rs815259
Chromosome Location	chr10:96976889-96976890
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:96975681..96977490-chr10:97052151..97054934,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PDLIM1-3	chr10:96976459-96978173	ucscGeneNc_uc001kkg_1

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10882570	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10882571	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12262534	0.92[EUR][1000 genomes]
rs12764831	0.82[EUR][1000 genomes]
rs12764992	0.82[EUR][1000 genomes]
rs2478480	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs489807	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs509736	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs513661	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs519833	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs589801	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs591171	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs592055	0.81[ASN][1000 genomes]
rs594448	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs595420	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs595478	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs600929	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs602941	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs610579	0.82[ASN][1000 genomes]
rs610837	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs611343	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs611371	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs612490	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs621299	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs627173	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs627719	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs628102	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs631107	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs632361	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs632979	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs633345	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs637465	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs637939	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs648695	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs649770	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs659949	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs660026	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs664093	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs667499	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs669360	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs685607	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs688706	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs689207	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs701886	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs815250	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs815267	0.89[ASN][1000 genomes]
rs9420648	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv497859	chr10:96058024-97027747	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv529726	chr10:96632494-97106315	Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	esv21432	chr10:96856006-96996043	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	esv1834151	chr10:96925446-96992955	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	esv15160	chr10:96942869-97074756	Bivalent Enhancer Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:96944200-96990400	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr10:96949800-96980600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr10:96956200-96979000	Weak transcription	Pancreas	Pancrea
4	chr10:96956200-96990400	Weak transcription	Aorta	Aorta
5	chr10:96960200-96988800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr10:96961800-96989400	Weak transcription	Primary T cells from cord blood	blood
7	chr10:96962000-96990000	Weak transcription	Fetal Intestine Small	intestine
8	chr10:96965000-96988000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr10:96965400-96983000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr10:96965400-96989400	Weak transcription	Fetal Intestine Large	intestine
11	chr10:96969200-96979400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr10:96969200-96979600	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr10:96969200-96990200	Weak transcription	Left Ventricle	heart
14	chr10:96969400-96977400	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr10:96969400-96980200	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr10:96969400-96980200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr10:96969400-96980400	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr10:96969400-96981600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr10:96969400-96984800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr10:96969400-96990400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr10:96970200-96992400	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr10:96971800-96989400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr10:96972000-96977400	Weak transcription	NHLF	lung
24	chr10:96972200-96988000	Weak transcription	Adipose Nuclei	Adipose
25	chr10:96972400-96977400	Weak transcription	HSMMtube	muscle
26	chr10:96972400-96987400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr10:96972400-96987800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr10:96972600-96977400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr10:96972600-96989600	Weak transcription	Fetal Thymus	thymus
30	chr10:96973600-96981000	Weak transcription	Gastric	stomach
31	chr10:96974800-96977400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr10:96974800-96981000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr10:96975000-96977200	Weak transcription	HSMM	muscle
34	chr10:96975000-96977400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr10:96975000-96977400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr10:96975000-96977400	Weak transcription	NHDF-Ad	bronchial
37	chr10:96975200-96977400	Weak transcription	NH-A	brain
38	chr10:96975200-96977400	Weak transcription	NHEK	skin
39	chr10:96975400-96977200	Weak transcription	Osteobl	bone
40	chr10:96975400-96980600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr10:96975400-96990200	Weak transcription	Primary hematopoietic stem cells	blood
42	chr10:96975600-96977200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr10:96975600-96979000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
44	chr10:96975600-96990000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr10:96975800-96981000	Weak transcription	Duodenum Mucosa	Duodenum
46	chr10:96976000-96990000	Weak transcription	Primary B cells from cord blood	blood
47	chr10:96976200-96981200	Weak transcription	Primary B cells from peripheral blood	blood
48	chr10:96976400-96978400	Enhancers	Muscle Satellite Cultured Cells	--
49	chr10:96976400-96978600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr10:96976400-96989600	Weak transcription	GM12878-XiMat	blood

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