Variant report

Variant	rs55865869
Chromosome Location	chr19:38069585-38069586
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:38068606..38070757-chr19:38083819..38085850,2	MCF-7	breast:
2	chr19:38068003..38069811-chr19:38073783..38075414,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171817	Chromatin interaction
ENSG00000180479	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10445548	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1048505	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1061753	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1061756	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12151156	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17244713	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17244769	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17303902	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17304703	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17305193	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17305228	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17305823	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17306900	0.86[ASN][1000 genomes]
rs1871196	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2291001	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2306201	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2385005	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35153242	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55681348	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55718806	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55743020	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55754546	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55909413	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56277404	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56351266	0.86[ASN][1000 genomes]
rs57654288	0.99[EUR][1000 genomes]
rs57943942	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62108291	0.84[EUR][1000 genomes]
rs62108306	0.82[EUR][1000 genomes]
rs7245855	0.86[ASN][1000 genomes]
rs7259272	0.82[EUR][1000 genomes]
rs73031330	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73033122	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73033134	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73033142	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73035159	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73035160	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73039029	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73041006	0.86[ASN][1000 genomes]
rs8101610	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8104282	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8104994	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8108268	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8111790	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv579468	chr19:37977609-38293487	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs55865869	AC012309.5	cis	Heart Left Ventricle	GTEx
rs55865869	AC012309.5	cis	lung	GTEx
rs55865869	AC012309.5	cis	Skin Sun Exposed Lower leg	GTEx
rs55865869	AC012309.5	cis	Thyroid	GTEx
rs55865869	AC012309.5	cis	Muscle Skeletal	GTEx
rs55865869	AC012309.5	cis	Artery Tibial	GTEx
rs55865869	AC012309.5	cis	Esophagus Muscularis	GTEx
rs55865869	ZNF585A	Cis_1M	lymphoblastoid	RTeQTL
rs55865869	AC012309.5	cis	Esophagus Mucosa	GTEx
rs55865869	ZNF781	cis	Thyroid	GTEx

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38032400-38080800	ZNF genes & repeats	Liver	Liver
2	chr19:38032600-38075200	ZNF genes & repeats	Adipose Nuclei	Adipose
3	chr19:38038000-38078400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr19:38038600-38079600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
5	chr19:38041200-38079600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr19:38045000-38078600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr19:38046400-38071800	ZNF genes & repeats	Brain Hippocampus Middle	brain
8	chr19:38046600-38079600	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
9	chr19:38047400-38078600	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
10	chr19:38049200-38079600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
11	chr19:38051600-38077600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
12	chr19:38051600-38078800	ZNF genes & repeats	Fetal Brain Female	brain
13	chr19:38052200-38075200	ZNF genes & repeats	Primary B cells from peripheral blood	blood
14	chr19:38052200-38078600	ZNF genes & repeats	Primary B cells from cord blood	blood
15	chr19:38053200-38078200	ZNF genes & repeats	Brain Germinal Matrix	brain
16	chr19:38053200-38078600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr19:38053400-38078400	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
18	chr19:38059800-38078000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
19	chr19:38065200-38078800	ZNF genes & repeats	Colon Smooth Muscle	Colon
20	chr19:38065800-38078400	ZNF genes & repeats	Primary T cells from cord blood	blood
21	chr19:38065800-38078600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
22	chr19:38066000-38072000	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
23	chr19:38066200-38069800	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr19:38066800-38071200	Weak transcription	Fetal Heart	heart
25	chr19:38067000-38077200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr19:38067800-38070600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr19:38068200-38070200	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
28	chr19:38068200-38071600	ZNF genes & repeats	Brain Anterior Caudate	brain
29	chr19:38068200-38078200	ZNF genes & repeats	Stomach Smooth Muscle	stomach
30	chr19:38068400-38071800	ZNF genes & repeats	Brain Substantia Nigra	brain
31	chr19:38068400-38071800	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
32	chr19:38068400-38073200	Weak transcription	HSMMtube	muscle
33	chr19:38068400-38073400	ZNF genes & repeats	Primary T helper naive cells from peripheral blood	blood
34	chr19:38068400-38078000	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
35	chr19:38068400-38078200	ZNF genes & repeats	Fetal Muscle Leg	muscle
36	chr19:38068400-38078400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr19:38068400-38078600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr19:38068400-38078800	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
39	chr19:38068600-38070200	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr19:38068600-38070400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr19:38068600-38070400	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr19:38068600-38070400	ZNF genes & repeats	Esophagus	oesophagus
43	chr19:38068600-38070400	ZNF genes & repeats	Fetal Intestine Small	intestine
44	chr19:38068600-38070400	ZNF genes & repeats	Fetal Stomach	stomach
45	chr19:38068600-38070400	ZNF genes & repeats	Lung	lung
46	chr19:38068600-38070400	ZNF genes & repeats	Rectal Smooth Muscle	rectum
47	chr19:38068600-38070600	ZNF genes & repeats	Left Ventricle	heart
48	chr19:38068600-38071000	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
49	chr19:38068600-38071400	Strong transcription	Psoas Muscle	Psoas
50	chr19:38068600-38071600	ZNF genes & repeats	Fetal Intestine Large	intestine

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