Variant report

Variant	rs57364495
Chromosome Location	chr4:20709411-20709412
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	chr4:20700245..20702604-chr4:20707211..20709448,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163138	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10516361	1.00[ASN][1000 genomes]
rs1061836	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1080125	0.88[ASN][1000 genomes]
rs11721944	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11723855	0.89[ASN][1000 genomes]
rs11733451	0.88[ASN][1000 genomes]
rs11735866	0.86[ASN][1000 genomes]
rs11736309	0.88[ASN][1000 genomes]
rs11736477	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11737893	0.92[ASN][1000 genomes]
rs12498799	0.88[ASN][1000 genomes]
rs12503714	1.00[ASN][1000 genomes]
rs12509329	0.90[ASN][1000 genomes]
rs12510666	0.94[ASN][1000 genomes]
rs1365580	0.96[ASN][1000 genomes]
rs1365581	0.96[ASN][1000 genomes]
rs1426882	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16869823	0.86[ASN][1000 genomes]
rs16869859	1.00[ASN][1000 genomes]
rs16869884	1.00[ASN][1000 genomes]
rs17552950	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17622121	0.92[ASN][1000 genomes]
rs2291530	0.89[ASN][1000 genomes]
rs28439580	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2874831	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56267013	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs59020971	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61790721	0.86[ASN][1000 genomes]
rs61790747	0.86[ASN][1000 genomes]
rs62410066	0.92[ASN][1000 genomes]
rs62410087	0.92[ASN][1000 genomes]
rs62410132	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62410133	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62410158	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62411661	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6831523	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73101456	0.92[ASN][1000 genomes]
rs964020	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][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	nsv1013077	chr4:20599841-20732558	Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1010145	chr4:20601908-21057992	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv537052	chr4:20601908-21057992	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv1014941	chr4:20611726-21345226	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	nsv537053	chr4:20611726-21345226	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
6	nsv829876	chr4:20638736-20835621	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS 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 miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs57364495	C4orf28	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:20702400-20722600	Weak transcription	Spleen	Spleen
2	chr4:20702600-20717200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:20703000-20717200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr4:20703000-20717400	Weak transcription	Fetal Heart	heart
5	chr4:20703000-20721800	Weak transcription	Rectal Smooth Muscle	rectum
6	chr4:20703000-20722800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr4:20703000-20741400	Weak transcription	Stomach Mucosa	stomach
8	chr4:20703200-20714400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr4:20703200-20715000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr4:20703200-20722800	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr4:20703200-20741000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr4:20703400-20722800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr4:20703400-20722800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr4:20703400-20723600	Weak transcription	Pancreas	Pancrea
15	chr4:20703400-20724000	Weak transcription	A549	lung
16	chr4:20703600-20715000	Weak transcription	Ovary	ovary
17	chr4:20703600-20716200	Weak transcription	Hela-S3	cervix
18	chr4:20703600-20717200	Weak transcription	Brain Germinal Matrix	brain
19	chr4:20703800-20714800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr4:20705000-20718200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr4:20705400-20718200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr4:20705600-20709800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr4:20705600-20715400	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr4:20706000-20711200	Strong transcription	Primary T cells from cord blood	blood
25	chr4:20706000-20711200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr4:20706000-20711200	Strong transcription	Skeletal Muscle Female	skeletal muscle
27	chr4:20706000-20712000	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr4:20706000-20712200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr4:20706000-20715200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr4:20706000-20715400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr4:20706000-20717400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr4:20706200-20709600	Strong transcription	Primary B cells from cord blood	blood
33	chr4:20706200-20709800	Strong transcription	Osteobl	bone
34	chr4:20706200-20710000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr4:20706200-20711200	Strong transcription	Stomach Smooth Muscle	stomach
36	chr4:20706200-20711400	Strong transcription	Adipose Nuclei	Adipose
37	chr4:20706200-20711600	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr4:20706200-20711600	Strong transcription	Liver	Liver
39	chr4:20706200-20711600	Strong transcription	Duodenum Mucosa	Duodenum
40	chr4:20706200-20711800	Strong transcription	Placenta	Placenta
41	chr4:20706200-20712000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr4:20706200-20712000	Strong transcription	Duodenum Smooth Muscle	Duodenum
43	chr4:20706200-20712400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr4:20706200-20712800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr4:20706200-20713400	Strong transcription	Fetal Lung	lung
46	chr4:20706200-20714000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr4:20706200-20715200	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr4:20706200-20715400	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr4:20706200-20715600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr4:20706200-20715600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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