Variant report

Variant	rs56251160
Chromosome Location	chr19:38471580-38471581
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:38420982..38422890-chr19:38471015..38472804,2	MCF-7	breast:
2	chr19:38421146..38425969-chr19:38469812..38473788,8	MCF-7	breast:
3	chr19:38470130..38474074-chr19:38479565..38484723,5	MCF-7	breast:
4	chr19:38429570..38433364-chr19:38470420..38473384,4	MCF-7	breast:
5	chr19:38459331..38461760-chr19:38470604..38472306,2	MCF-7	breast:
6	chr19:38394269..38398486-chr19:38470778..38473091,3	MCF-7	breast:
7	chr19:38395951..38398517-chr19:38469657..38472006,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171804	Chromatin interaction
ENSG00000105738	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs17249336	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs55752822	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55785437	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55813548	0.81[AMR][1000 genomes]
rs55946812	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55974157	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs55983118	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55994045	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56080901	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56207124	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56230664	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56246446	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56252444	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56300335	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56676595	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6508755	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7245962	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7257266	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7258011	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73034922	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73036634	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73036658	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8100199	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS 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 target site	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs56251160	AC012309.5	cis	Esophagus Mucosa	GTEx
rs56251160	ZNF585A	Cis_1M	lymphoblastoid	RTeQTL
rs56251160	ZNF781	cis	Thyroid	GTEx
rs56251160	AC012309.5	cis	Heart Left Ventricle	GTEx
rs56251160	AC012309.5	cis	Artery Tibial	GTEx
rs56251160	AC012309.5	cis	Thyroid	GTEx

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38461600-38472000	Weak transcription	NHDF-Ad	bronchial
2	chr19:38461600-38476600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:38461600-38493600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr19:38461600-38493600	Weak transcription	Stomach Smooth Muscle	stomach
5	chr19:38461800-38476800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr19:38462200-38471800	Enhancers	Primary B cells from peripheral blood	blood
7	chr19:38463600-38476000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr19:38463800-38476200	Weak transcription	Primary hematopoietic stem cells	blood
9	chr19:38463800-38484800	Weak transcription	Fetal Stomach	stomach
10	chr19:38466000-38472400	Weak transcription	Primary T cells from cord blood	blood
11	chr19:38466000-38475800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr19:38467800-38471800	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr19:38468000-38472000	Enhancers	Primary B cells from cord blood	blood
14	chr19:38468200-38473600	Enhancers	Lung	lung
15	chr19:38468200-38474200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr19:38468200-38474600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr19:38468200-38475600	Enhancers	HMEC	breast
18	chr19:38468200-38475800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr19:38468200-38483600	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr19:38468400-38473000	Enhancers	NH-A	brain
21	chr19:38468400-38473200	Enhancers	HSMM	muscle
22	chr19:38468800-38474000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr19:38469000-38474200	Enhancers	Fetal Intestine Large	intestine
24	chr19:38469200-38474800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr19:38469200-38479600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr19:38469800-38475800	Genic enhancers	Fetal Intestine Small	intestine
27	chr19:38470000-38472800	Enhancers	Brain Inferior Temporal Lobe	brain
28	chr19:38470200-38472000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr19:38470200-38472200	Enhancers	Duodenum Mucosa	Duodenum
30	chr19:38470200-38472200	Enhancers	Rectal Mucosa Donor 29	rectum
31	chr19:38470200-38472600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr19:38470200-38473200	Enhancers	Fetal Lung	lung
33	chr19:38470200-38474200	Enhancers	Sigmoid Colon	Sigmoid Colon
34	chr19:38470200-38474200	Enhancers	Stomach Mucosa	stomach
35	chr19:38470200-38474400	Enhancers	Rectal Mucosa Donor 31	rectum
36	chr19:38470400-38471600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr19:38470400-38471600	Enhancers	Fetal Muscle Leg	muscle
38	chr19:38470400-38471600	Enhancers	Spleen	Spleen
39	chr19:38470400-38471800	Enhancers	Brain Anterior Caudate	brain
40	chr19:38470400-38471800	Enhancers	Brain Hippocampus Middle	brain
41	chr19:38470400-38471800	Enhancers	Brain Substantia Nigra	brain
42	chr19:38470400-38471800	Enhancers	Colonic Mucosa	Colon
43	chr19:38470400-38471800	Enhancers	Psoas Muscle	Psoas
44	chr19:38470400-38472200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr19:38470400-38472400	Enhancers	Brain Angular Gyrus	brain
46	chr19:38470400-38472600	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr19:38470400-38473600	Enhancers	Pancreas	Pancrea
48	chr19:38470400-38474400	Enhancers	Esophagus	oesophagus
49	chr19:38470400-38474800	Enhancers	Gastric	stomach
50	chr19:38470600-38471600	Enhancers	Skeletal Muscle Male	skeletal muscle

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