Variant report

Variant	rs12460570
Chromosome Location	chr19:20003576-20003577
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	chr19:20002691..20004301-chr19:20008482..20010852,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF506-2	chr19:20002764-20004041	ENSG00000245381

Extended variants
information (count: 44 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1008112	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1019280	0.82[EUR][1000 genomes]
rs11085283	0.82[EUR][1000 genomes]
rs11666112	0.82[EUR][1000 genomes]
rs11668581	0.81[EUR][1000 genomes]
rs12151060	0.82[EUR][1000 genomes]
rs12608906	0.83[EUR][1000 genomes]
rs12610295	0.82[EUR][1000 genomes]
rs2110587	0.89[EUR][1000 genomes]
rs2110589	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2160157	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2335365	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4809005	0.83[EUR][1000 genomes]
rs4809007	0.83[EUR][1000 genomes]
rs4809014	0.82[EUR][1000 genomes]
rs55739609	0.82[ASN][1000 genomes]
rs55816500	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57490026	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58151139	0.83[EUR][1000 genomes]
rs7254966	0.80[ASN][1000 genomes]
rs7255064	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7258113	0.80[ASN][1000 genomes]
rs73008668	0.83[EUR][1000 genomes]
rs73008670	0.83[EUR][1000 genomes]
rs73532705	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8109457	0.83[EUR][1000 genomes]
rs8111124	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063273	chr19:19591146-20061367	ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv911314	chr19:19866371-20021046	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv519535	chr19:19871250-20595412	Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
4	nsv911315	chr19:19872093-20021046	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv911316	chr19:19890450-20021046	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv961192	chr19:19906394-20083740	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	esv3319016	chr19:19917475-20819154	Weak transcription ZNF genes & repeats Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
8	esv3319017	chr19:19917475-20819154	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
9	esv3413756	chr19:19936066-20072059	ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	esv3380276	chr19:19936583-20073601	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	esv3429980	chr19:19943721-20102072	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic 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	15 gene(s)	inside rSNPs	diseases
12	nsv1061846	chr19:19946927-20595412	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
13	esv3390957	chr19:19965887-20819154	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	53 gene(s)	inside rSNPs	diseases
14	nsv869122	chr19:19969851-20595412	ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
15	nsv1057569	chr19:19973268-20193556	Enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
16	nsv1059158	chr19:19973489-20576161	Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases
17	esv3407363	chr19:20000919-20059307	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12460570	ZNF253	cis	Nerve Tibial	GTEx
rs12460570	ZNF253	Cis_1M	lymphoblastoid	RTeQTL
rs12460570	ZNF253	cis	Heart Left Ventricle	GTEx
rs12460570	ZNF506	Cis_1M	lymphoblastoid	RTeQTL
rs12460570	ZNF682	cis	Muscle Skeletal	GTEx

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19977600-20006800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:19978800-20007600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr19:19979000-20004000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
4	chr19:19979200-20007400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr19:19979400-20008200	ZNF genes & repeats	Liver	Liver
6	chr19:19986800-20004800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr19:19988600-20003800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr19:19989600-20007400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr19:19990800-20007000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr19:19991000-20006200	ZNF genes & repeats	Brain Germinal Matrix	brain
11	chr19:19991800-20005600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
12	chr19:19992200-20006200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr19:19994800-20007600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr19:19995000-20006800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
15	chr19:19995600-20004000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr19:19996200-20003600	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
17	chr19:19996600-20004000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
18	chr19:19996600-20004200	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr19:19996600-20005400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
20	chr19:19996600-20005400	ZNF genes & repeats	Dnd41	blood
21	chr19:19996600-20005400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
22	chr19:19996800-20004000	ZNF genes & repeats	Primary B cells from peripheral blood	blood
23	chr19:19996800-20004800	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr19:19996800-20006400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
25	chr19:19998000-20003600	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
26	chr19:19998000-20004000	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
27	chr19:19998200-20003600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
28	chr19:19998200-20003600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr19:19998200-20003600	ZNF genes & repeats	Fetal Muscle Trunk	muscle
30	chr19:19998200-20003800	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
31	chr19:19998200-20004000	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
32	chr19:19998200-20007000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
33	chr19:19998800-20004800	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
34	chr19:19998800-20005000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr19:19998800-20006400	ZNF genes & repeats	Fetal Brain Female	brain
36	chr19:19999000-20004000	ZNF genes & repeats	Brain Hippocampus Middle	brain
37	chr19:19999000-20004400	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
38	chr19:19999000-20004600	ZNF genes & repeats	Adipose Nuclei	Adipose
39	chr19:19999000-20005400	ZNF genes & repeats	Fetal Lung	lung
40	chr19:19999400-20003800	ZNF genes & repeats	Brain Substantia Nigra	brain
41	chr19:19999600-20003800	ZNF genes & repeats	HSMMtube	muscle
42	chr19:20000200-20004200	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr19:20000200-20004800	ZNF genes & repeats	Primary T cells from cord blood	blood
44	chr19:20000400-20004200	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
45	chr19:20000400-20005400	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr19:20000600-20004800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr19:20000600-20004800	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
48	chr19:20000800-20004000	ZNF genes & repeats	HepG2	liver
49	chr19:20001000-20003800	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr19:20001000-20003800	ZNF genes & repeats	Fetal Kidney	kidney

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