Variant report

Variant	rs28528757
Chromosome Location	chr19:36732215-36732216
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:36729380..36732375-chr19:36732759..36734481,3	MCF-7	breast:
2	chr19:36730136..36732594-chr19:36734296..36737243,2	K562	blood:

Variant related genes	Relation type
ENSG00000196357	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10403738	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10407835	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10407850	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10409983	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10412832	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10415410	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10416509	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10416742	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10416925	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10419269	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10425166	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11882933	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12459704	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12460466	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12461077	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12461112	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12461855	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12463157	0.84[AMR][1000 genomes]
rs28414272	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4361039	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4806284	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4806293	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4806294	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4806295	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4806303	0.85[AMR][1000 genomes]
rs55697131	0.87[AMR][1000 genomes]
rs56206115	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56316708	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56686317	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57385903	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57734651	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs59026641	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59295196	0.94[ASN][1000 genomes]
rs61413061	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62113093	0.85[EUR][1000 genomes]
rs62113146	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62113148	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62113149	0.84[AMR][1000 genomes]
rs62113151	0.85[AMR][1000 genomes]
rs62113152	0.84[AMR][1000 genomes]
rs7251745	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73038028	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73040107	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73040113	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73040148	0.84[AMR][1000 genomes]
rs73041817	0.82[AMR][1000 genomes]
rs8106135	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8111860	0.89[EUR][1000 genomes];0.82[ASN][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	esv3526489	chr19:36306483-36741945	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
2	esv3526490	chr19:36306483-36741945	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	nsv520020	chr19:36721368-36822594	Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv9715	chr19:36729688-36811749	Weak transcription Active TSS Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs28528757	ZNF545	Cis_1M	lymphoblastoid	RTeQTL
rs28528757	CTD-3162L10.1	cis	Muscle Skeletal	GTEx
rs28528757	LINC00665	cis	Muscle Skeletal	GTEx

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36721000-36735800	Weak transcription	Right Atrium	heart
2	chr19:36724400-36735800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr19:36728200-36735800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr19:36728200-36735800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr19:36728200-36736000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr19:36728400-36735800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr19:36728400-36735800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr19:36728400-36735800	Weak transcription	Brain Anterior Caudate	brain
9	chr19:36728400-36735800	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr19:36728400-36735800	Weak transcription	Brain Substantia Nigra	brain
11	chr19:36728400-36736200	Weak transcription	Gastric	stomach
12	chr19:36728600-36735800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr19:36728600-36735800	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr19:36728600-36735800	Weak transcription	Brain Cingulate Gyrus	brain
15	chr19:36728600-36735800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr19:36728600-36736000	Weak transcription	Left Ventricle	heart
17	chr19:36728600-36736000	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr19:36728800-36735800	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr19:36728800-36735800	Weak transcription	NHLF	lung
20	chr19:36729000-36734800	Weak transcription	NHEK	skin
21	chr19:36729000-36735800	Weak transcription	Fetal Heart	heart
22	chr19:36729200-36735800	Weak transcription	Fetal Brain Male	brain
23	chr19:36729200-36735800	Weak transcription	Fetal Kidney	kidney
24	chr19:36729400-36734200	Weak transcription	NHDF-Ad	bronchial
25	chr19:36729400-36735800	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr19:36729400-36735800	Weak transcription	HMEC	breast
27	chr19:36729400-36735800	Weak transcription	Osteobl	bone
28	chr19:36729400-36736000	Weak transcription	Brain Hippocampus Middle	brain
29	chr19:36729600-36735800	Weak transcription	Fetal Lung	lung
30	chr19:36729800-36734400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr19:36729800-36736000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr19:36730000-36735800	Weak transcription	Brain Germinal Matrix	brain
33	chr19:36730000-36735800	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr19:36730000-36735800	Weak transcription	Rectal Smooth Muscle	rectum
35	chr19:36730000-36736000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr19:36730200-36735800	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr19:36730200-36735800	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr19:36730200-36736000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr19:36730400-36735800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr19:36730400-36735800	Weak transcription	HUVEC	blood vessel
41	chr19:36730400-36736000	Weak transcription	Right Ventricle	heart
42	chr19:36730400-36748400	Weak transcription	HSMMtube	muscle
43	chr19:36730600-36735600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr19:36730600-36735800	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr19:36730600-36735800	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr19:36730600-36735800	Weak transcription	Brain Angular Gyrus	brain
47	chr19:36730600-36736000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr19:36730600-36736000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr19:36730600-36736000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr19:36730600-36736000	Weak transcription	Ovary	ovary

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