Variant report

Variant	rs28565512
Chromosome Location	chr4:57397196-57397197
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:57331864..57334391-chr4:57396918..57398546,3	MCF-7	breast:
2	chr4:57297760..57299581-chr4:57396785..57398752,2	MCF-7	breast:
3	chr4:57332142..57335262-chr4:57394352..57398997,8	K562	blood:
4	chr4:57331783..57334990-chr4:57394745..57398997,7	K562	blood:
5	chr4:57299474..57303800-chr4:57395386..57399526,7	K562	blood:
6	chr4:57298757..57303397-chr4:57395270..57398462,7	K562	blood:
7	chr4:57396793..57399968-chr4:57400354..57402510,5	K562	blood:
8	chr4:57251883..57253946-chr4:57396755..57399062,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000269921	Chromatin interaction
ENSG00000128059	Chromatin interaction
ENSG00000157426	Chromatin interaction
ENSG00000174780	Chromatin interaction
ENSG00000128050	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10013766	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10023933	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13150614	0.89[ASN][1000 genomes]
rs28541354	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28561081	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28624866	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4280802	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57688783	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66662206	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
4	nsv530121	chr4:57167367-57695576	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
5	nsv829941	chr4:57359551-57553136	Weak transcription Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	esv3447654	chr4:57395445-57397943	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs28565512	SRP72	Cis_1M	lymphoblastoid	RTeQTL
rs28565512	PPAT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57395800-57397200	Active TSS	Brain Anterior Caudate	brain
2	chr4:57396200-57397200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr4:57396200-57397200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr4:57396200-57397200	Active TSS	Brain Angular Gyrus	brain
5	chr4:57396200-57397200	Active TSS	Brain Cingulate Gyrus	brain
6	chr4:57396200-57397200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr4:57396200-57397200	Active TSS	Colon Smooth Muscle	Colon
8	chr4:57396200-57397200	Active TSS	Duodenum Smooth Muscle	Duodenum
9	chr4:57396200-57397200	Active TSS	Fetal Brain Female	brain
10	chr4:57396200-57397200	Active TSS	Fetal Heart	heart
11	chr4:57396200-57397200	Bivalent/Poised TSS	Fetal Intestine Small	intestine
12	chr4:57396200-57397200	Active TSS	Fetal Lung	lung
13	chr4:57396200-57397200	Active TSS	Rectal Mucosa Donor 29	rectum
14	chr4:57396200-57397200	Active TSS	A549	lung
15	chr4:57396200-57397400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
16	chr4:57396200-57397400	Active TSS	Breast Myoepithelial Primary Cells	Breast
17	chr4:57396200-57397400	Active TSS	Primary T helper naive cells from peripheral blood	blood
18	chr4:57396200-57397400	Active TSS	Brain Substantia Nigra	brain
19	chr4:57396200-57397400	Active TSS	Psoas Muscle	Psoas
20	chr4:57396200-57397400	Active TSS	NHDF-Ad	bronchial
21	chr4:57396200-57397600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
22	chr4:57396200-57397600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr4:57396200-57397600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
24	chr4:57396200-57397600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
25	chr4:57396200-57397600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr4:57396200-57397600	Flanking Active TSS	Primary hematopoietic stem cells	blood
27	chr4:57396200-57397600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
28	chr4:57396200-57397600	Active TSS	Aorta	Aorta
29	chr4:57396200-57397600	Active TSS	Brain Inferior Temporal Lobe	brain
30	chr4:57396200-57397600	Active TSS	Pancreatic Islets	Pancreatic Islet
31	chr4:57396200-57397800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
32	chr4:57396200-57397800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr4:57396200-57397800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
34	chr4:57396200-57397800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
35	chr4:57396200-57397800	Bivalent/Poised TSS	Fetal Kidney	kidney
36	chr4:57396200-57398000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
37	chr4:57396200-57398000	Active TSS	Rectal Smooth Muscle	rectum
38	chr4:57396200-57398200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr4:57396400-57397200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
40	chr4:57396400-57397200	Active TSS	Primary T killer memory cells from peripheral blood	blood
41	chr4:57396400-57397200	Active TSS	Liver	Liver
42	chr4:57396400-57397200	Active TSS	Esophagus	oesophagus
43	chr4:57396400-57397200	Active TSS	Gastric	stomach
44	chr4:57396400-57397200	Active TSS	Thymus	Thymus
45	chr4:57396400-57397600	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr4:57396400-57397600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr4:57396400-57397600	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr4:57396400-57397600	Enhancers	Spleen	Spleen
49	chr4:57396400-57397600	Bivalent/Poised TSS	HSMMtube	muscle
50	chr4:57396400-57397800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell

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