Variant report

Variant	rs28485784
Chromosome Location	chr4:7859874-7859875
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	chr4:7857940..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]
rs28400396	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:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7830400-7862600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:7830600-7862200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr4:7830600-7862400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr4:7843600-7863000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr4:7845000-7863200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:7846200-7860200	Weak transcription	Small Intestine	intestine
7	chr4:7848000-7872200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr4:7848200-7862000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr4:7851800-7860400	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr4:7852000-7860400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr4:7852600-7873600	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr4:7855200-7863400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr4:7855600-7863200	Weak transcription	Hela-S3	cervix
14	chr4:7855800-7862400	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr4:7856200-7860400	Weak transcription	Pancreas	Pancrea
16	chr4:7856200-7862200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr4:7856200-7872800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr4:7856400-7860400	Weak transcription	Gastric	stomach
19	chr4:7856400-7861400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr4:7856400-7865600	Weak transcription	Duodenum Mucosa	Duodenum
21	chr4:7856400-7865800	Weak transcription	Brain Cingulate Gyrus	brain
22	chr4:7856600-7862600	Genic enhancers	A549	lung
23	chr4:7856600-7863200	Weak transcription	Fetal Kidney	kidney
24	chr4:7856800-7860000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr4:7857000-7860800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr4:7857000-7862400	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr4:7857200-7861600	Enhancers	HUVEC	blood vessel
28	chr4:7857200-7862000	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr4:7857200-7862200	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr4:7857200-7862200	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr4:7857200-7863200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr4:7857200-7864800	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr4:7857400-7860000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr4:7857400-7860800	Enhancers	Right Atrium	heart
35	chr4:7857400-7862200	Weak transcription	Placenta	Placenta
36	chr4:7857600-7860800	Enhancers	HMEC	breast
37	chr4:7857600-7873000	Weak transcription	Colonic Mucosa	Colon
38	chr4:7857800-7860400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr4:7857800-7860400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr4:7857800-7860400	Enhancers	Primary T killer memory cells from peripheral blood	blood
41	chr4:7857800-7860600	Enhancers	Primary T helper cells PMA-I stimulated	--
42	chr4:7857800-7861600	Weak transcription	Fetal Intestine Small	intestine
43	chr4:7857800-7862000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr4:7857800-7862200	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr4:7857800-7862200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr4:7857800-7896400	Weak transcription	Spleen	Spleen
47	chr4:7858000-7860800	Enhancers	Cortex derived primary cultured neurospheres	brain
48	chr4:7858000-7860800	Enhancers	Placenta Amnion	Placenta Amnion
49	chr4:7858400-7860000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr4:7858400-7860600	Enhancers	Fetal Brain Female	brain

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