Variant report

Variant	rs10409983
Chromosome Location	chr19:36716806-36716807
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:36716744-36717335	PFSK-1	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:36705638..36707650-chr19:36715342..36717503,2	MCF-7	breast:
2	chr19:36713025..36717797-chr19:36719610..36723880,4	K562	blood:

Variant related genes	Relation type
ZNF146	TF binding region
ENSG00000167635	Chromatin interaction
ENSG00000196357	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10403738	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10407835	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10407850	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10412832	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10415410	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10416509	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10416742	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10416925	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10419269	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10425166	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11882933	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12459704	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12460466	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12461077	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12461112	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12461855	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28414272	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28528757	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4361039	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4806284	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4806293	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4806294	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4806295	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56206115	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56316708	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56686317	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57385903	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57734651	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59026641	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59295196	0.96[ASN][1000 genomes]
rs61413061	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62113093	0.86[EUR][1000 genomes]
rs62113146	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62113148	0.83[ASN][1000 genomes]
rs7251745	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73038028	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73040107	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73040113	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8106135	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8111860	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3526489	chr19:36306483-36741945	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
2	esv3526490	chr19:36306483-36741945	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10409983	CTD-3162L10.1	cis	Muscle Skeletal	GTEx
rs10409983	ZNF545	Cis_1M	lymphoblastoid	RTeQTL
rs10409983	LINC00665	cis	Muscle Skeletal	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36707000-36726800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:36707400-36730200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:36707600-36731800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr19:36707800-36717000	Weak transcription	HSMMtube	muscle
5	chr19:36708000-36719800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr19:36708200-36730800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr19:36709000-36723000	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr19:36709000-36723800	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr19:36709000-36724000	Strong transcription	H1 Cell Line	embryonic stem cell
10	chr19:36709400-36723800	Strong transcription	Fetal Muscle Trunk	muscle
11	chr19:36710000-36725000	ZNF genes & repeats	GM12878-XiMat	blood
12	chr19:36710000-36732200	ZNF genes & repeats	A549	lung
13	chr19:36710000-36732200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
14	chr19:36710200-36720600	Strong transcription	Fetal Thymus	thymus
15	chr19:36710800-36719000	Weak transcription	Fetal Brain Male	brain
16	chr19:36710800-36719400	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr19:36710800-36721800	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
18	chr19:36710800-36723200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr19:36711000-36723200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
20	chr19:36711000-36723400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr19:36711000-36724000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr19:36711200-36728400	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
23	chr19:36711600-36719400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr19:36711800-36719400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr19:36711800-36725000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr19:36711800-36726600	Strong transcription	Fetal Muscle Leg	muscle
27	chr19:36713000-36730200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
28	chr19:36713200-36717000	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr19:36713200-36719000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr19:36713400-36726600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr19:36714000-36718400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr19:36714000-36719000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr19:36714000-36731000	Strong transcription	Dnd41	blood
34	chr19:36714400-36731400	ZNF genes & repeats	Liver	Liver
35	chr19:36714600-36717200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
36	chr19:36714800-36717200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr19:36715000-36717000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr19:36715000-36717000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
39	chr19:36715000-36717200	Genic enhancers	Fetal Stomach	stomach
40	chr19:36715000-36717800	Enhancers	Brain Hippocampus Middle	brain
41	chr19:36715200-36717000	Genic enhancers	Duodenum Smooth Muscle	Duodenum
42	chr19:36715200-36723600	Strong transcription	Placenta	Placenta
43	chr19:36715200-36731200	Strong transcription	Fetal Brain Female	brain
44	chr19:36715200-36731600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
45	chr19:36715400-36717000	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr19:36715400-36721200	Strong transcription	K562	blood
47	chr19:36715400-36724200	Strong transcription	Hela-S3	cervix
48	chr19:36715800-36717200	Enhancers	Ovary	ovary
49	chr19:36715800-36726800	ZNF genes & repeats	Fetal Intestine Small	intestine
50	chr19:36716000-36717200	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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