Variant report

Variant	rs28400396
Chromosome Location	chr4:7858454-7858455
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:7857940..7860738-chr4:7861450..7863442,2	K562	blood:
2	chr4:7858124..7860265-chr4:7863996..7865854,2	K562	blood:

Variant related genes	Relation type
ENSG00000196526	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs28376459	0.82[EUR][1000 genomes]
rs28394500	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28485784	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28504337	0.82[EUR][1000 genomes]
rs28542303	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28552075	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28584083	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28650789	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28699608	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28729656	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28738908	0.81[EUR][1000 genomes]
rs61292547	0.82[EUR][1000 genomes]
rs7441783	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][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	nsv491712	chr4:7582506-8155069	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv34140	chr4:7787936-8172491	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats 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	18 gene(s)	inside rSNPs	diseases
3	esv2754386	chr4:7822449-7992909	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv2756298	chr4:7822449-7992909	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv878578	chr4:7841833-7969594	Enhancers Flanking Active TSS Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7821200-7859000	Weak transcription	Aorta	Aorta
2	chr4:7830400-7862600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:7830600-7862200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr4:7830600-7862400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr4:7843600-7863000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr4:7845000-7858600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr4:7845000-7863200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr4:7845200-7859000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr4:7846200-7860200	Weak transcription	Small Intestine	intestine
10	chr4:7848000-7872200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr4:7848200-7862000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr4:7851800-7860400	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr4:7852000-7860400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr4:7852600-7873600	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr4:7853800-7859200	Enhancers	Skeletal Muscle Female	skeletal muscle
16	chr4:7854000-7858600	Genic enhancers	HSMM	muscle
17	chr4:7854000-7859000	Genic enhancers	Osteobl	bone
18	chr4:7855000-7858800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr4:7855200-7863400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr4:7855400-7859400	Strong transcription	NHEK	skin
21	chr4:7855600-7858600	Genic enhancers	HSMMtube	muscle
22	chr4:7855600-7863200	Weak transcription	Hela-S3	cervix
23	chr4:7855800-7862400	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr4:7856200-7859200	Weak transcription	Brain Hippocampus Middle	brain
25	chr4:7856200-7860400	Weak transcription	Pancreas	Pancrea
26	chr4:7856200-7862200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr4:7856200-7872800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr4:7856400-7860400	Weak transcription	Gastric	stomach
29	chr4:7856400-7861400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr4:7856400-7865600	Weak transcription	Duodenum Mucosa	Duodenum
31	chr4:7856400-7865800	Weak transcription	Brain Cingulate Gyrus	brain
32	chr4:7856600-7862600	Genic enhancers	A549	lung
33	chr4:7856600-7863200	Weak transcription	Fetal Kidney	kidney
34	chr4:7856800-7858600	Enhancers	Adipose Nuclei	Adipose
35	chr4:7856800-7860000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr4:7857000-7858600	Genic enhancers	Muscle Satellite Cultured Cells	--
37	chr4:7857000-7860800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr4:7857000-7862400	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr4:7857200-7858600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
40	chr4:7857200-7858800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr4:7857200-7859400	Enhancers	Primary T cells fromperipheralblood	blood
42	chr4:7857200-7859600	Enhancers	Left Ventricle	heart
43	chr4:7857200-7861600	Enhancers	HUVEC	blood vessel
44	chr4:7857200-7862000	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr4:7857200-7862200	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr4:7857200-7862200	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr4:7857200-7863200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr4:7857200-7864800	Enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr4:7857400-7858600	Weak transcription	Fetal Lung	lung
50	chr4:7857400-7859000	Enhancers	Primary T helper naive cells from peripheral blood	blood

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