Variant report

Variant	rs576779
Chromosome Location	chr4:56274307-56274308
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:56268360-56274870	K562	blood:	n/a	n/a
2	POLR2A	chr4:56274234-56274841	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr4:56273145-56274893	IMR90	lung:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:56272858..56275843-chr4:56602241..56604494,2	K562	blood:
2	chr4:56274229..56276308-chr4:56282213..56284888,2	MCF-7	breast:
3	chr4:56212034..56214727-chr4:56273890..56277792,4	MCF-7	breast:
4	chr4:56272499..56275145-chr4:56296679..56299422,2	K562	blood:
5	chr4:56269741..56272367-chr4:56273938..56276057,3	MCF-7	breast:
6	chr4:56211324..56213872-chr4:56274081..56277036,2	K562	blood:
7	chr4:56273385..56275386-chr4:56294557..56296512,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000239040	TF binding region
ENSG00000128039	Chromatin interaction
ENSG00000134851	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10005989	0.86[AMR][1000 genomes]
rs10034433	0.81[AMR][1000 genomes]
rs1011095	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10462035	0.84[EUR][1000 genomes]
rs11133376	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11133379	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11133382	0.83[EUR][1000 genomes]
rs11133383	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11733864	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11735267	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11931061	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11939815	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11947476	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11947623	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12646078	0.83[EUR][1000 genomes]
rs12647034	0.81[EUR][1000 genomes]
rs13102385	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13121235	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13128582	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13138697	0.85[EUR][1000 genomes]
rs13152650	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1522106	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1522107	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1522108	0.84[EUR][1000 genomes]
rs1522110	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1522111	0.86[EUR][1000 genomes]
rs17085889	0.86[AMR][1000 genomes]
rs1965467	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1980273	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2140077	0.85[EUR][1000 genomes]
rs2177129	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2412646	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2412647	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28514423	0.82[AMR][1000 genomes]
rs28525309	0.82[AMR][1000 genomes]
rs28582059	0.84[AMR][1000 genomes]
rs28665088	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28726308	0.81[EUR][1000 genomes]
rs35767091	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3736544	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3736545	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3805147	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3805152	0.84[EUR][1000 genomes]
rs3805154	0.85[EUR][1000 genomes]
rs3805157	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3817444	0.84[EUR][1000 genomes]
rs3828481	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4371676	0.82[EUR][1000 genomes]
rs4580704	0.86[EUR][1000 genomes]
rs473005	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs480479	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4864998	0.85[EUR][1000 genomes]
rs491381	0.82[AFR][1000 genomes]
rs564762	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62303714	0.86[EUR][1000 genomes]
rs6810948	0.80[EUR][1000 genomes]
rs6811520	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6815516	0.86[AMR][1000 genomes]
rs6817267	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6819660	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6824057	0.83[EUR][1000 genomes]
rs6824955	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6825994	0.83[AMR][1000 genomes]
rs6832769	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6834676	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6837710	0.84[EUR][1000 genomes]
rs6839788	0.82[AMR][1000 genomes]
rs6846427	0.83[EUR][1000 genomes]
rs6851838	0.84[AMR][1000 genomes]
rs6853192	0.81[AMR][1000 genomes]
rs7660054	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7667849	0.81[EUR][1000 genomes]
rs7668147	0.87[AMR][1000 genomes]
rs7670225	0.84[EUR][1000 genomes]
rs7673908	0.86[AMR][1000 genomes]
rs7677526	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7684810	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7692795	0.82[AFR][1000 genomes]
rs819271	0.81[EUR][1000 genomes]
rs9312662	0.83[EUR][1000 genomes]
rs9993675	0.82[EUR][1000 genomes]
rs9997288	0.85[EUR][1000 genomes]
rs9998038	0.84[AMR][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	esv3328582	chr4:56164136-56486156	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv999477	chr4:56219035-56397180	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv537101	chr4:56219035-56397180	Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv1011722	chr4:56261349-56325600	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56264800-56282200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr4:56264800-56292200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr4:56265600-56275600	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr4:56265600-56281600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr4:56265600-56283800	Weak transcription	Fetal Brain Male	brain
6	chr4:56265600-56286000	Weak transcription	Colonic Mucosa	Colon
7	chr4:56265600-56289800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr4:56265600-56319800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr4:56265800-56274400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr4:56265800-56275200	Weak transcription	Fetal Heart	heart
11	chr4:56265800-56281200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr4:56266000-56283200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr4:56266200-56275600	Weak transcription	Right Ventricle	heart
14	chr4:56267400-56275200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr4:56267400-56280800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr4:56267400-56282800	Weak transcription	Small Intestine	intestine
17	chr4:56267400-56283200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr4:56267600-56275800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr4:56267600-56280800	Weak transcription	A549	lung
20	chr4:56268800-56326000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr4:56269000-56274400	Strong transcription	HSMM	muscle
22	chr4:56269000-56311400	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr4:56269200-56274600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr4:56269200-56275000	Strong transcription	Fetal Thymus	thymus
25	chr4:56269400-56274600	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr4:56269400-56274800	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr4:56269800-56274600	Strong transcription	Sigmoid Colon	Sigmoid Colon
28	chr4:56270000-56274400	Strong transcription	Fetal Muscle Trunk	muscle
29	chr4:56270000-56281000	Weak transcription	Fetal Kidney	kidney
30	chr4:56270200-56274800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr4:56270200-56281000	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr4:56270200-56281600	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr4:56270200-56282800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr4:56270400-56277400	Weak transcription	Hela-S3	cervix
35	chr4:56270400-56286400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr4:56271200-56275400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr4:56271800-56277800	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr4:56272000-56274400	Genic enhancers	Brain Angular Gyrus	brain
39	chr4:56272000-56274600	Genic enhancers	Brain Cingulate Gyrus	brain
40	chr4:56272400-56275600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr4:56272400-56275800	Weak transcription	Colon Smooth Muscle	Colon
42	chr4:56272400-56276000	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr4:56272400-56278000	Weak transcription	Esophagus	oesophagus
44	chr4:56272400-56281000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr4:56272600-56274400	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr4:56272600-56275200	Weak transcription	Brain Anterior Caudate	brain
47	chr4:56272600-56275200	Weak transcription	NHEK	skin
48	chr4:56272600-56277800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr4:56272600-56282800	Weak transcription	Primary hematopoietic stem cells	blood
50	chr4:56272800-56275600	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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