Variant report

Variant	rs13345148
Chromosome Location	chr19:37819631-37819632
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:37819186..37820687-chr19:37835807..37837449,2	MCF-7	breast:
2	chr19:37808613..37811422-chr19:37818380..37821776,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF527-1	chr19:37819127-37820601	ENSG00000248454
2	lnc-ZNF527-1	chr19:37819481-37820007	NONHSAT066100

Variant related genes	Relation type
ENSG00000181666	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs1015848	0.82[EUR][1000 genomes]
rs1015849	0.82[EUR][1000 genomes]
rs1035479	0.84[EUR][1000 genomes]
rs10403582	0.80[EUR][1000 genomes]
rs10403613	0.97[EUR][1000 genomes]
rs10404602	0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10404920	0.91[EUR][1000 genomes]
rs10405064	0.95[EUR][1000 genomes]
rs10405325	0.87[EUR][1000 genomes]
rs10405407	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10406177	0.82[EUR][1000 genomes]
rs10407084	0.82[EUR][1000 genomes]
rs10409204	0.84[EUR][1000 genomes]
rs10412043	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10413602	0.85[EUR][1000 genomes]
rs10414904	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10415024	0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10415358	0.98[EUR][1000 genomes]
rs10415937	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10417503	0.97[EUR][1000 genomes]
rs10417844	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10420430	0.85[EUR][1000 genomes]
rs10422074	0.85[EUR][1000 genomes]
rs10422423	0.97[EUR][1000 genomes]
rs10422667	0.82[EUR][1000 genomes]
rs10422967	0.97[EUR][1000 genomes]
rs10424574	0.96[EUR][1000 genomes]
rs10426297	0.92[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs10426618	0.82[EUR][1000 genomes]
rs10426666	0.96[EUR][1000 genomes]
rs10426699	0.98[EUR][1000 genomes]
rs11671972	0.85[ASN][1000 genomes]
rs12104380	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12104381	0.95[EUR][1000 genomes]
rs12709812	0.89[EUR][1000 genomes]
rs12709813	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12972252	0.82[EUR][1000 genomes]
rs12979470	0.83[EUR][1000 genomes]
rs12981532	0.85[EUR][1000 genomes]
rs12982333	0.91[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs13343471	0.84[EUR][1000 genomes]
rs13343485	0.90[EUR][1000 genomes]
rs13343502	0.81[EUR][1000 genomes]
rs13345116	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1373991	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1559229	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1823061	0.93[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2112923	0.82[EUR][1000 genomes]
rs2303131	0.84[EUR][1000 genomes]
rs28402338	0.97[EUR][1000 genomes]
rs28538699	0.81[EUR][1000 genomes]
rs28623164	0.83[EUR][1000 genomes]
rs2891699	0.83[EUR][1000 genomes]
rs34544865	0.83[EUR][1000 genomes]
rs34603719	0.83[EUR][1000 genomes]
rs35085437	0.97[EUR][1000 genomes]
rs35777021	0.84[EUR][1000 genomes]
rs3745765	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3760825	0.82[EUR][1000 genomes]
rs3803895	0.84[EUR][1000 genomes]
rs4417644	0.97[EUR][1000 genomes]
rs4452075	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4801759	0.82[EUR][1000 genomes]
rs4801803	0.81[EUR][1000 genomes]
rs4803229	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4803347	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4803460	0.84[EUR][1000 genomes]
rs4803539	0.84[EUR][1000 genomes]
rs4969487	0.97[EUR][1000 genomes]
rs57795776	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6508711	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6508713	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6508714	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6508715	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6508716	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6508719	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs67293224	0.89[EUR][1000 genomes]
rs713256	0.93[EUR][1000 genomes]
rs7246993	0.85[EUR][1000 genomes]
rs7247259	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7252099	0.84[EUR][1000 genomes]
rs7252325	0.83[EUR][1000 genomes]
rs7252346	0.83[EUR][1000 genomes]
rs7255407	0.83[EUR][1000 genomes]
rs7255972	0.84[EUR][1000 genomes]
rs7256130	0.81[EUR][1000 genomes]
rs7257495	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7257672	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7258692	0.98[EUR][1000 genomes]
rs7259968	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7408133	0.98[EUR][1000 genomes]
rs7408446	0.93[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs7408563	0.98[EUR][1000 genomes]
rs8109632	0.83[EUR][1000 genomes]
rs8111782	0.91[EUR][1000 genomes]
rs8112610	0.81[EUR][1000 genomes]
rs9304566	0.97[EUR][1000 genomes]
rs9676967	0.83[EUR][1000 genomes]
rs9917081	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv918028	chr19:37020645-38014526	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	nsv978811	chr19:37749967-37820517	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv2757695	chr19:37794850-38051606	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	esv2758759	chr19:37794850-38051606	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37809200-37824800	Weak transcription	Stomach Mucosa	stomach
2	chr19:37809400-37825000	Weak transcription	Fetal Thymus	thymus
3	chr19:37809400-37825000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr19:37809600-37824400	Weak transcription	NHDF-Ad	bronchial
5	chr19:37809600-37825000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr19:37809800-37820000	Weak transcription	HMEC	breast
7	chr19:37810000-37820000	Weak transcription	NHLF	lung
8	chr19:37810000-37825000	Weak transcription	Hela-S3	cervix
9	chr19:37810200-37821800	ZNF genes & repeats	A549	lung
10	chr19:37810400-37821000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr19:37810400-37821600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr19:37810600-37824400	Weak transcription	Small Intestine	intestine
13	chr19:37810600-37824800	Weak transcription	Fetal Heart	heart
14	chr19:37810800-37824200	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr19:37811000-37821400	Strong transcription	Fetal Stomach	stomach
16	chr19:37811600-37820200	Weak transcription	NH-A	brain
17	chr19:37811600-37821000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr19:37811600-37821200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr19:37811600-37825000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr19:37811800-37821600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr19:37812200-37821000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr19:37812600-37820600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr19:37812600-37820800	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr19:37812600-37821000	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr19:37813000-37821400	Strong transcription	Stomach Smooth Muscle	stomach
26	chr19:37813200-37821200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr19:37813200-37821400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr19:37813200-37821400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr19:37813200-37821400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr19:37813200-37821400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr19:37813200-37821800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr19:37813400-37820400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr19:37813400-37821600	Strong transcription	Fetal Muscle Trunk	muscle
34	chr19:37813400-37821600	Strong transcription	Skeletal Muscle Female	skeletal muscle
35	chr19:37813400-37821600	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr19:37813600-37820800	Strong transcription	Primary T helper cells PMA-I stimulated	--
37	chr19:37813600-37821400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr19:37813800-37820200	Strong transcription	Dnd41	blood
39	chr19:37813800-37820600	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
40	chr19:37813800-37820800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr19:37813800-37821400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr19:37813800-37821600	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr19:37813800-37821800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr19:37813800-37821800	Strong transcription	Fetal Intestine Large	intestine
45	chr19:37814000-37821600	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr19:37814400-37820200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
47	chr19:37814400-37821000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr19:37814400-37821200	Strong transcription	HUES6 Cell Line	embryonic stem cell
49	chr19:37814400-37821200	Strong transcription	Duodenum Mucosa	Duodenum
50	chr19:37814400-37821600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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