Variant report

Variant	rs55974157
Chromosome Location	chr19:38412494-38412495
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:38412344..38414154-chr19:38421844..38424438,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000105738	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs12150862	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12151082	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17248097	0.81[EUR][1000 genomes]
rs17248670	0.82[EUR][1000 genomes]
rs17249138	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17249336	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3859549	0.81[EUR][1000 genomes]
rs4536583	0.81[EUR][1000 genomes]
rs4614853	0.84[AMR][1000 genomes]
rs55752822	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55785437	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs55813548	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55946812	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs55983118	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55994045	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56080901	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56184201	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56207124	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56230664	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56233644	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56246446	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56251160	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56252444	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56268127	0.81[EUR][1000 genomes]
rs56300335	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56676595	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6508755	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7245962	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7257266	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7258011	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73027472	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73027480	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73034922	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73036634	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73036658	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73041036	0.81[EUR][1000 genomes]
rs7343065	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8100199	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8110293	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
4	nsv1061106	chr19:38400149-38448723	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv544001	chr19:38400149-38448723	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs55974157	AC012309.5	cis	Thyroid	GTEx
rs55974157	ZNF585A	Cis_1M	lymphoblastoid	RTeQTL
rs55974157	ZNF781	cis	Thyroid	GTEx
rs55974157	AC012309.5	cis	Esophagus Muscularis	GTEx
rs55974157	AC012309.5	cis	Heart Left Ventricle	GTEx
rs55974157	AC012309.5	cis	Esophagus Mucosa	GTEx
rs55974157	AC012309.5	cis	Muscle Skeletal	GTEx
rs55974157	AC012309.5	cis	Artery Tibial	GTEx

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38398600-38422600	Weak transcription	Aorta	Aorta
2	chr19:38398800-38433800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr19:38399000-38418400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr19:38399000-38422400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr19:38399200-38415600	Weak transcription	Hela-S3	cervix
6	chr19:38399200-38416000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr19:38399200-38422400	Weak transcription	Rectal Smooth Muscle	rectum
8	chr19:38399200-38422600	Weak transcription	Fetal Lung	lung
9	chr19:38399200-38424600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr19:38399600-38422000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr19:38399600-38424000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr19:38399600-38424200	Weak transcription	Right Atrium	heart
13	chr19:38399600-38441200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr19:38399800-38413800	Weak transcription	Liver	Liver
15	chr19:38399800-38417200	Weak transcription	Ovary	ovary
16	chr19:38399800-38421200	Weak transcription	Gastric	stomach
17	chr19:38399800-38421800	Weak transcription	Left Ventricle	heart
18	chr19:38399800-38422400	Weak transcription	Fetal Brain Female	brain
19	chr19:38399800-38422600	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr19:38400000-38422000	Weak transcription	HSMM	muscle
21	chr19:38400400-38416800	Weak transcription	Pancreas	Pancrea
22	chr19:38400400-38419400	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr19:38400400-38421800	Weak transcription	Fetal Muscle Trunk	muscle
24	chr19:38400600-38422000	Weak transcription	HSMMtube	muscle
25	chr19:38400600-38422400	Weak transcription	HUVEC	blood vessel
26	chr19:38400800-38422400	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr19:38401000-38416600	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr19:38401000-38421600	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr19:38401200-38416800	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr19:38401200-38421200	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr19:38402000-38416800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr19:38402000-38422600	Weak transcription	Fetal Brain Male	brain
33	chr19:38404200-38416800	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr19:38405200-38422600	Weak transcription	Right Ventricle	heart
35	chr19:38405600-38422800	Weak transcription	Colon Smooth Muscle	Colon
36	chr19:38406000-38413600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr19:38406000-38416600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr19:38406000-38417200	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr19:38406000-38418800	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr19:38406000-38419400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr19:38406000-38422600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr19:38406400-38413800	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr19:38406400-38415800	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr19:38406400-38418200	Weak transcription	Fetal Heart	heart
45	chr19:38406400-38418600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr19:38406400-38419200	Weak transcription	Colonic Mucosa	Colon
47	chr19:38406600-38414200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr19:38407200-38417400	Genic enhancers	Primary B cells from peripheral blood	blood
49	chr19:38410200-38413600	Weak transcription	Dnd41	blood
50	chr19:38410200-38413600	Weak transcription	NHDF-Ad	bronchial

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