Variant report

Variant	rs10412832
Chromosome Location	chr19:36708586-36708587
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	chr19:36708343-36708607	MCF10A-Er-Src	breast:	n/a	n/a
2	PAX5	chr19:36708481-36708808	GM12878	blood:	n/a	n/a
3	POLR2A	chr19:36708477-36708746	HepG2	liver:	n/a	n/a
4	POLR2A	chr19:36708520-36708643	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:36706883..36709067-chr19:36978381..36980309,2	K562	blood:
2	chr19:36706964..36709175-chr20:49993312..49995838,2	MCF-7	breast:
3	chr19:36705207..36708225-chr19:36708519..36712657,6	K562	blood:
4	chr19:36545669..36547627-chr19:36708408..36710754,2	K562	blood:

Variant related genes	Relation type
ZNF565	TF binding region
ENSG00000075702	Chromatin interaction
ENSG00000196357	Chromatin interaction
ENSG00000263645	Chromatin interaction
ENSG00000167635	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	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10407835	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10407850	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10409983	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10415410	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10416509	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10416742	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10416925	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10419269	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10425166	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11882933	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[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	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12461077	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12461112	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12461855	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28414272	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28528757	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4361039	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4806284	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4806293	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4806294	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4806295	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56206115	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56316708	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56686317	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57385903	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57734651	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59026641	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59295196	0.96[ASN][1000 genomes]
rs61413061	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62113093	0.83[EUR][1000 genomes]
rs62113146	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62113148	0.83[ASN][1000 genomes]
rs7251745	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73038028	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73040107	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73040113	0.84[ASN][1000 genomes]
rs8106135	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8111860	0.88[AMR][1000 genomes];0.87[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
rs10412832	CTD-3162L10.1	cis	Muscle Skeletal	GTEx
rs10412832	LINC00665	cis	Muscle Skeletal	GTEx
rs10412832	ZNF545	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36706800-36708600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr19:36706800-36709800	Weak transcription	Lung	lung
3	chr19:36706800-36710800	Weak transcription	Esophagus	oesophagus
4	chr19:36706800-36716400	Weak transcription	Aorta	Aorta
5	chr19:36707000-36708600	Enhancers	Fetal Brain Male	brain
6	chr19:36707000-36708600	Weak transcription	Right Atrium	heart
7	chr19:36707000-36708800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr19:36707000-36709000	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr19:36707000-36709200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr19:36707000-36709800	Enhancers	Primary T cells fromperipheralblood	blood
11	chr19:36707000-36709800	Weak transcription	Placenta	Placenta
12	chr19:36707000-36710000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr19:36707000-36710000	Weak transcription	Fetal Intestine Large	intestine
14	chr19:36707000-36710200	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr19:36707000-36711000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr19:36707000-36711800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr19:36707000-36711800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr19:36707000-36711800	Weak transcription	Colonic Mucosa	Colon
19	chr19:36707000-36712800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr19:36707000-36712800	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr19:36707000-36716200	Weak transcription	Rectal Smooth Muscle	rectum
22	chr19:36707000-36726800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr19:36707200-36709000	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr19:36707200-36709200	Enhancers	Primary T cells from cord blood	blood
25	chr19:36707200-36710000	Weak transcription	Duodenum Mucosa	Duodenum
26	chr19:36707200-36710000	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr19:36707200-36710000	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr19:36707200-36710400	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr19:36707200-36712600	Weak transcription	NHDF-Ad	bronchial
30	chr19:36707400-36708600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr19:36707400-36708600	Enhancers	HepG2	liver
32	chr19:36707400-36709400	Weak transcription	Thymus	Thymus
33	chr19:36707400-36710000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr19:36707400-36710000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr19:36707400-36710200	Weak transcription	Fetal Thymus	thymus
36	chr19:36707400-36710800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr19:36707400-36730200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr19:36707600-36708600	Strong transcription	Fetal Intestine Small	intestine
39	chr19:36707600-36708600	ZNF genes & repeats	A549	lung
40	chr19:36707600-36708600	ZNF genes & repeats	GM12878-XiMat	blood
41	chr19:36707600-36709000	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr19:36707600-36709800	Weak transcription	Primary hematopoietic stem cells	blood
43	chr19:36707600-36710200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr19:36707600-36711600	Weak transcription	NHEK	skin
45	chr19:36707600-36711800	Weak transcription	Primary B cells from cord blood	blood
46	chr19:36707600-36712400	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr19:36707600-36712800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr19:36707600-36713000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr19:36707600-36731800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr19:36707800-36709000	Weak transcription	HUES48 Cell Line	embryonic stem cell

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