Variant report

Variant	rs28457189
Chromosome Location	chr4:87855104-87855105
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	IRF1	chr4:87855042-87856705	K562	blood:	n/a	chr4:87856113-87856127 chr4:87856094-87856108 chr4:87855197-87855207 chr4:87856479-87856493
2	TBL1XR1	chr4:87854932-87856388	K562	blood:	n/a	n/a
3	CREB1	chr4:87855101-87855676	H1-hESC	embryonic stem cell:	n/a	n/a
4	MAZ	chr4:87855096-87858341	GM12878	blood:	n/a	chr4:87856044-87856054 chr4:87856093-87856103
5	POLR2A	chr4:87854895-87858502	GM12891	blood:	n/a	n/a
6	POLR2A	chr4:87855041-87855143	K562	blood:	n/a	n/a
7	POLR2A	chr4:87855069-87858042	K562	blood:	n/a	n/a
8	ZC3H11A	chr4:87855004-87856001	K562	blood:	n/a	n/a
9	POLR2A	chr4:87854677-87858857	MCF10A-Er-Src	breast:	n/a	n/a
10	JUN	chr4:87854283-87858230	K562	blood:	n/a	chr4:87858106-87858115 chr4:87857423-87857432 chr4:87857427-87857435 chr4:87857424-87857433
11	HCFC1	chr4:87855064-87858107	Hela-S3	cervix:	n/a	n/a
12	ARID3A	chr4:87854949-87856353	K562	blood:	n/a	n/a
13	POLR2A	chr4:87854999-87857944	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:87854791..87857074-chr4:87968149..87971029,2	K562	blood:
2	chr4:87854638..87857344-chr4:88139505..88141852,2	K562	blood:
3	chr4:87845889..87863516-chr4:87925389..87935181,79	K562	blood:
4	chr4:87853595..87871697-chr4:87924007..87941983,77	K562	blood:
5	chr4:87853395..87861870-chr4:87925425..87930611,18	MCF-7	breast:
6	chr4:87854708..87860113-chr4:87926348..87930107,23	MCF-7	breast:

Variant related genes	Relation type
AFF1	TF binding region
ENSG00000172493	Chromatin interaction
ENSG00000145332	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10029698	0.94[EUR][1000 genomes]
rs10034541	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1075989	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12186239	0.92[EUR][1000 genomes]
rs13103212	0.88[EUR][1000 genomes]
rs13112444	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13114907	0.82[EUR][1000 genomes]
rs13117826	0.88[EUR][1000 genomes]
rs13131035	0.92[EUR][1000 genomes]
rs13131194	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13134746	0.88[EUR][1000 genomes]
rs13143520	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13147942	0.88[EUR][1000 genomes]
rs13151671	0.94[EUR][1000 genomes]
rs13151797	0.88[EUR][1000 genomes]
rs13434404	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2705623	0.88[EUR][1000 genomes]
rs28407685	0.94[EUR][1000 genomes]
rs28439108	0.88[EUR][1000 genomes]
rs28447475	0.88[EUR][1000 genomes]
rs28458234	0.97[EUR][1000 genomes]
rs28502831	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs28594717	0.97[EUR][1000 genomes]
rs28610346	0.94[EUR][1000 genomes]
rs28620528	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28629974	0.92[EUR][1000 genomes]
rs28661703	0.90[EUR][1000 genomes]
rs28664715	0.92[EUR][1000 genomes]
rs28706796	0.97[EUR][1000 genomes]
rs28729679	0.88[EUR][1000 genomes]
rs28854225	0.92[EUR][1000 genomes]
rs28886889	0.92[EUR][1000 genomes]
rs34077745	0.82[AMR][1000 genomes]
rs34991149	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35480728	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35667731	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs36053558	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71605624	0.85[EUR][1000 genomes]
rs71605686	0.88[EUR][1000 genomes]
rs71605687	0.88[EUR][1000 genomes]
rs71605688	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs71605691	0.94[EUR][1000 genomes]
rs71605693	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7683045	0.88[EUR][1000 genomes]
rs9993812	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9999001	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][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	nsv594787	chr4:87221827-87888667	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1013308	chr4:87769694-87870168	Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv508297	chr4:87778783-87868508	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv1009937	chr4:87795314-88008345	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87825800-87855200	Weak transcription	Fetal Stomach	stomach
2	chr4:87830200-87855200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr4:87842600-87855400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:87845800-87855200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr4:87846400-87855400	Weak transcription	Gastric	stomach
6	chr4:87849400-87855200	Weak transcription	Thymus	Thymus
7	chr4:87849600-87855400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr4:87849800-87855200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr4:87849800-87855400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr4:87849800-87855400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr4:87849800-87855400	Weak transcription	Esophagus	oesophagus
12	chr4:87849800-87855400	Weak transcription	Lung	lung
13	chr4:87849800-87855800	Weak transcription	Spleen	Spleen
14	chr4:87850400-87855200	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr4:87851200-87855200	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr4:87851400-87855200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr4:87851400-87855200	Weak transcription	Fetal Muscle Trunk	muscle
18	chr4:87852400-87855200	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr4:87852800-87855200	Weak transcription	Left Ventricle	heart
20	chr4:87852800-87855200	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr4:87852800-87855400	Weak transcription	Pancreas	Pancrea
22	chr4:87854400-87855200	Enhancers	Brain Cingulate Gyrus	brain
23	chr4:87854400-87855200	Enhancers	Fetal Intestine Small	intestine
24	chr4:87854400-87855400	Enhancers	Liver	Liver
25	chr4:87854400-87855800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr4:87854600-87857000	Active TSS	Placenta	Placenta
27	chr4:87854800-87855200	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr4:87854800-87855200	Enhancers	Primary B cells from cord blood	blood
29	chr4:87854800-87855200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr4:87854800-87855200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr4:87854800-87855200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr4:87854800-87855200	Enhancers	Primary T killer memory cells from peripheral blood	blood
33	chr4:87854800-87855200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr4:87854800-87855200	Flanking Active TSS	Brain Hippocampus Middle	brain
35	chr4:87854800-87855200	Enhancers	Brain Inferior Temporal Lobe	brain
36	chr4:87854800-87855200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
37	chr4:87854800-87855200	Flanking Active TSS	Colon Smooth Muscle	Colon
38	chr4:87854800-87855200	Enhancers	Fetal Thymus	thymus
39	chr4:87854800-87855200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
40	chr4:87854800-87855200	Flanking Active TSS	GM12878-XiMat	blood
41	chr4:87854800-87855200	Flanking Active TSS	Hela-S3	cervix
42	chr4:87854800-87855200	Enhancers	HSMM	muscle
43	chr4:87854800-87855200	Flanking Active TSS	NHDF-Ad	bronchial
44	chr4:87854800-87855200	Enhancers	NHLF	lung
45	chr4:87854800-87855400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
46	chr4:87854800-87855400	Enhancers	Primary B cells from peripheral blood	blood
47	chr4:87854800-87855400	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
48	chr4:87854800-87855600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr4:87854800-87855600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr4:87854800-87855800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood

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