Variant report

Variant	rs55813548
Chromosome Location	chr19:38399940-38399941
allele	C/T
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	chr19:38396652-38400700	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:38395556..38401665-chr19:38419693..38425913,12	MCF-7	breast:
2	chr19:38399136..38401318-chr19:38404847..38407238,2	MCF-7	breast:
3	chr19:38393450..38400778-chr19:38419865..38427350,17	MCF-7	breast:

Variant related genes	Relation type
WDR87	TF binding region
ENSG00000105738	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs12150862	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12151082	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17248097	0.81[EUR][1000 genomes]
rs17248670	0.82[EUR][1000 genomes]
rs17249138	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17249336	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3859549	0.81[EUR][1000 genomes]
rs4536583	0.81[EUR][1000 genomes]
rs4614853	0.81[AMR][1000 genomes]
rs55752822	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55785437	0.85[AMR][1000 genomes]
rs55974157	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55983118	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56080901	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56184201	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56207124	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56230664	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56233644	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56246446	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56251160	0.81[AMR][1000 genomes]
rs56252444	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs56268127	0.81[EUR][1000 genomes]
rs56300335	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56676595	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6508755	0.83[AMR][1000 genomes]
rs7245962	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7257266	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7258011	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73027472	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73027480	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73034922	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73036634	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs73036658	0.84[AMR][1000 genomes]
rs73041036	0.81[EUR][1000 genomes]
rs7343065	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8100199	0.83[AMR][1000 genomes]
rs8110293	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
2	nsv833820	chr19:38190721-38414049	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv1064401	chr19:38387797-38427984	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats 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	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs55813548	AC012309.5	cis	Esophagus Mucosa	GTEx
rs55813548	AC012309.5	cis	Muscle Skeletal	GTEx
rs55813548	ZNF585A	Cis_1M	lymphoblastoid	RTeQTL
rs55813548	AC012309.5	cis	Heart Left Ventricle	GTEx
rs55813548	ZNF781	cis	Thyroid	GTEx
rs55813548	AC012309.5	cis	Artery Tibial	GTEx
rs55813548	AC012309.5	cis	Esophagus Muscularis	GTEx
rs55813548	AC012309.5	cis	Thyroid	GTEx

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38396400-38400600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr19:38397000-38401000	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr19:38398600-38422600	Weak transcription	Aorta	Aorta
4	chr19:38398800-38400000	Enhancers	Sigmoid Colon	Sigmoid Colon
5	chr19:38398800-38400400	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr19:38398800-38400400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
7	chr19:38398800-38400400	Enhancers	Fetal Muscle Trunk	muscle
8	chr19:38398800-38400400	Enhancers	Fetal Thymus	thymus
9	chr19:38398800-38400400	Enhancers	Pancreas	Pancrea
10	chr19:38398800-38400600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr19:38398800-38405200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr19:38398800-38433800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr19:38399000-38400000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr19:38399000-38400000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr19:38399000-38400200	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr19:38399000-38400200	Enhancers	Fetal Brain Male	brain
17	chr19:38399000-38400400	Enhancers	H9 Cell Line	embryonic stem cell
18	chr19:38399000-38400400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr19:38399000-38400600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr19:38399000-38400800	Enhancers	HepG2	liver
21	chr19:38399000-38401200	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr19:38399000-38418400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr19:38399000-38422400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr19:38399200-38400000	Enhancers	Brain Inferior Temporal Lobe	brain
25	chr19:38399200-38400000	Enhancers	Fetal Intestine Large	intestine
26	chr19:38399200-38400200	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr19:38399200-38400200	Weak transcription	Psoas Muscle	Psoas
28	chr19:38399200-38400200	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr19:38399200-38400400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr19:38399200-38400400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr19:38399200-38400400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
32	chr19:38399200-38400600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr19:38399200-38400600	Enhancers	HSMMtube	muscle
34	chr19:38399200-38400600	Enhancers	HUVEC	blood vessel
35	chr19:38399200-38400800	Enhancers	iPS-15b Cell Line	embryonic stem cell
36	chr19:38399200-38401000	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr19:38399200-38401200	Enhancers	H1 Cell Line	embryonic stem cell
38	chr19:38399200-38401200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr19:38399200-38401400	Enhancers	iPS-20b Cell Line	embryonic stem cell
40	chr19:38399200-38401400	Weak transcription	HMEC	breast
41	chr19:38399200-38401800	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr19:38399200-38402800	Weak transcription	Fetal Intestine Small	intestine
43	chr19:38399200-38404800	Weak transcription	Primary T cells from cord blood	blood
44	chr19:38399200-38405000	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr19:38399200-38405400	Weak transcription	Adipose Nuclei	Adipose
46	chr19:38399200-38405400	Weak transcription	Fetal Muscle Leg	muscle
47	chr19:38399200-38405400	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr19:38399200-38409400	Weak transcription	Stomach Smooth Muscle	stomach
49	chr19:38399200-38411000	Weak transcription	Brain Cingulate Gyrus	brain
50	chr19:38399200-38411000	Weak transcription	Stomach Mucosa	stomach

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