Variant report

Variant	rs56207124
Chromosome Location	chr19:38423600-38423601
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:38395556..38401665-chr19:38419693..38425913,12	MCF-7	breast:
2	chr19:38393450..38400778-chr19:38419865..38427350,17	MCF-7	breast:
3	chr19:38405526..38407086-chr19:38423053..38425586,2	MCF-7	breast:
4	chr19:38423561..38425591-chr19:38488215..38490133,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000105738	Chromatin interaction
ENSG00000171804	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs12150862	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12151082	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17248097	0.81[EUR][1000 genomes]
rs17248670	0.81[EUR][1000 genomes]
rs17249138	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17249336	0.94[AMR][1000 genomes];0.85[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];1.00[EUR][1000 genomes]
rs55785437	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs55813548	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55946812	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs55974157	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55983118	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55994045	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56080901	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56184201	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56230664	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56233644	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs56246446	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];0.83[EUR][1000 genomes]
rs56268127	0.81[EUR][1000 genomes]
rs56300335	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56676595	1.00[AMR][1000 genomes];0.99[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];0.91[EUR][1000 genomes]
rs7257266	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7258011	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73027472	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73027480	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73034922	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73036634	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73036658	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73041036	0.80[EUR][1000 genomes]
rs7343065	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8100199	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8110293	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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
3	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
4	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
rs56207124	ZNF585A	Cis_1M	lymphoblastoid	RTeQTL
rs56207124	AC012309.5	cis	Esophagus Mucosa	GTEx
rs56207124	AC012309.5	cis	Esophagus Muscularis	GTEx
rs56207124	AC012309.5	cis	Artery Tibial	GTEx
rs56207124	AC012309.5	cis	Heart Left Ventricle	GTEx
rs56207124	AC012309.5	cis	Muscle Skeletal	GTEx
rs56207124	AC012309.5	cis	Thyroid	GTEx
rs56207124	ZNF781	cis	Thyroid	GTEx

Chromatin state (count:140 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38398800-38433800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr19:38399200-38424600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr19:38399600-38424000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr19:38399600-38424200	Weak transcription	Right Atrium	heart
5	chr19:38399600-38441200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr19:38411800-38426200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr19:38412000-38423800	Weak transcription	Lung	lung
8	chr19:38418800-38425600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr19:38419400-38424800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr19:38420200-38425000	Weak transcription	Small Intestine	intestine
11	chr19:38421200-38424400	Enhancers	Fetal Heart	heart
12	chr19:38421200-38425000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr19:38421600-38424800	Enhancers	Fetal Thymus	thymus
14	chr19:38421800-38423800	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr19:38421800-38425400	Enhancers	Fetal Muscle Trunk	muscle
16	chr19:38421800-38425400	Enhancers	Fetal Muscle Leg	muscle
17	chr19:38422000-38426400	Weak transcription	Primary T cells from cord blood	blood
18	chr19:38422200-38425000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr19:38422200-38425600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr19:38422400-38423600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr19:38422400-38423600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
22	chr19:38422400-38423600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
23	chr19:38422400-38423600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
24	chr19:38422400-38423600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr19:38422400-38423600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr19:38422400-38423800	Flanking Active TSS	NHEK	skin
27	chr19:38422400-38424000	Flanking Active TSS	Primary B cells from cord blood	blood
28	chr19:38422400-38424200	Flanking Active TSS	GM12878-XiMat	blood
29	chr19:38422400-38424400	Active TSS	Rectal Smooth Muscle	rectum
30	chr19:38422400-38424600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr19:38422400-38424800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr19:38422400-38424800	Enhancers	Left Ventricle	heart
33	chr19:38422400-38424800	Enhancers	HUVEC	blood vessel
34	chr19:38422400-38425000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr19:38422400-38425000	Enhancers	Psoas Muscle	Psoas
36	chr19:38422400-38425000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
37	chr19:38422600-38423600	Flanking Active TSS	H1 Cell Line	embryonic stem cell
38	chr19:38422600-38423600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr19:38422600-38423600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
40	chr19:38422600-38423600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
41	chr19:38422600-38423600	Flanking Active TSS	Primary B cells from peripheral blood	blood
42	chr19:38422600-38423600	Flanking Active TSS	Primary hematopoietic stem cells	blood
43	chr19:38422600-38423600	Active TSS	Fetal Kidney	kidney
44	chr19:38422600-38423600	Flanking Active TSS	HMEC	breast
45	chr19:38422600-38424400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
46	chr19:38422600-38424400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
47	chr19:38422600-38425000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr19:38422800-38423600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
49	chr19:38422800-38423600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
50	chr19:38422800-38424000	Active TSS	Colonic Mucosa	Colon

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