Variant report

Variant	rs2571116
Chromosome Location	chr19:44995456-44995457
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	chr19:44983712..44985391-chr19:44995000..44997386,2	K562	blood:
2	chr19:44993270..44996512-chr19:44998152..45001010,3	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11670601	0.81[AFR][1000 genomes]
rs13343871	0.80[AFR][1000 genomes]
rs13344684	0.80[AFR][1000 genomes]
rs13344700	0.80[AFR][1000 genomes]
rs13345771	0.80[AFR][1000 genomes]
rs13345783	0.80[AFR][1000 genomes]
rs1865385	0.84[EUR][1000 genomes]
rs1897821	0.81[EUR][1000 genomes]
rs1897824	0.84[EUR][1000 genomes]
rs2117384	0.86[EUR][1000 genomes]
rs2461534	0.91[EUR][1000 genomes]
rs2571040	0.91[EUR][1000 genomes]
rs2571041	0.85[EUR][1000 genomes]
rs2571046	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2571048	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2571049	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2571050	0.86[EUR][1000 genomes]
rs2571053	0.82[EUR][1000 genomes]
rs2571115	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2686756	0.85[EUR][1000 genomes]
rs2686757	0.85[EUR][1000 genomes]
rs2686758	0.91[EUR][1000 genomes]
rs2686762	0.86[EUR][1000 genomes]
rs2686769	0.91[EUR][1000 genomes]
rs28394449	0.86[ASN][1000 genomes]
rs28482326	0.86[ASN][1000 genomes]
rs28599882	0.86[ASN][1000 genomes]
rs34400340	0.81[AFR][1000 genomes]
rs4802227	0.80[AFR][1000 genomes]
rs59202354	0.80[AFR][1000 genomes]
rs62118147	0.88[EUR][1000 genomes]
rs7250221	0.84[EUR][1000 genomes]
rs926020	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs954314	0.85[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	nsv912112	chr19:44853707-45011727	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv912114	chr19:44858776-45002563	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv1061350	chr19:44869075-45035469	Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv912115	chr19:44957508-44995990	ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers	TF binding region Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2571116	ZNF180	cis	Muscle Skeletal	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44978800-45003400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
2	chr19:44989000-44997000	Weak transcription	Hela-S3	cervix
3	chr19:44989200-44996800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr19:44991800-44996000	Weak transcription	Fetal Heart	heart
5	chr19:44992200-44996400	Weak transcription	NH-A	brain
6	chr19:44993600-45002000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr19:44993600-45002000	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
8	chr19:44993600-45003600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr19:44993600-45003600	ZNF genes & repeats	Primary B cells from cord blood	blood
10	chr19:44993600-45003600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
11	chr19:44993600-45003600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr19:44994000-44995600	ZNF genes & repeats	A549	lung
13	chr19:44994000-44998200	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr19:44994000-45000000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr19:44994000-45000000	ZNF genes & repeats	Fetal Kidney	kidney
16	chr19:44994000-45001800	ZNF genes & repeats	Dnd41	blood
17	chr19:44994000-45002200	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
18	chr19:44994000-45002200	ZNF genes & repeats	Brain Cingulate Gyrus	brain
19	chr19:44994000-45002600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
20	chr19:44994000-45002600	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
21	chr19:44994000-45002800	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
22	chr19:44994000-45002800	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
23	chr19:44994000-45002800	ZNF genes & repeats	Brain Anterior Caudate	brain
24	chr19:44994000-45002800	ZNF genes & repeats	HepG2	liver
25	chr19:44994000-45003000	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
26	chr19:44994000-45003000	ZNF genes & repeats	Fetal Brain Female	brain
27	chr19:44994000-45003000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
28	chr19:44994000-45003200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
29	chr19:44994000-45003200	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
30	chr19:44994000-45003200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr19:44994000-45003200	ZNF genes & repeats	Liver	Liver
32	chr19:44994000-45003400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr19:44994000-45003400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr19:44994000-45003400	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
35	chr19:44994000-45003600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
36	chr19:44994000-45003600	ZNF genes & repeats	GM12878-XiMat	blood
37	chr19:44994000-45003800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr19:44994000-45003800	ZNF genes & repeats	Brain Germinal Matrix	brain
39	chr19:44994200-44997000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr19:44994200-44997200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr19:44994200-45000200	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
42	chr19:44994200-45000200	ZNF genes & repeats	Stomach Smooth Muscle	stomach
43	chr19:44994200-45000400	ZNF genes & repeats	Left Ventricle	heart
44	chr19:44994200-45000800	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr19:44994200-45001200	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
46	chr19:44994200-45001200	ZNF genes & repeats	Primary T cells from cord blood	blood
47	chr19:44994200-45002000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr19:44994200-45002200	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr19:44994200-45002600	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
50	chr19:44994200-45002600	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood

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