Variant report

Variant	rs28628732
Chromosome Location	chr5:43071801-43071802
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:43071224-43071859	K562	blood:	n/a	n/a
2	POLR2A	chr5:43071641-43071817	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr5:43071467-43071885	HL-60	blood:	n/a	n/a
4	POLR2A	chr5:43071521-43071821	HepG2	liver:	n/a	n/a
5	POLR2A	chr5:43071565-43071876	MCF10A-Er-Src	breast:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr5:43070103..43072247-chr5:43117148..43119199,2	K562	blood:
2	chr5:43070295..43071835-chr5:43373758..43376387,2	MCF-7	breast:
3	chr5:43034726..43053192-chr5:43061725..43074206,66	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC114947.1.1-2	chr5:43071269-43076732	XLOC_004366

No data

Variant related genes	Relation type
ENSG00000177738	TF binding region
ENSG00000215068	Chromatin interaction
ENSG00000177721	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10051990	0.92[EUR][1000 genomes]
rs10052644	0.92[EUR][1000 genomes]
rs10054331	0.92[EUR][1000 genomes]
rs10056822	0.84[EUR][1000 genomes]
rs10064210	0.84[EUR][1000 genomes]
rs10071791	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1122510	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13357786	0.92[EUR][1000 genomes]
rs13357845	0.87[AFR][1000 genomes]
rs13360205	0.84[EUR][1000 genomes]
rs28573681	0.84[EUR][1000 genomes]
rs56917209	0.84[EUR][1000 genomes]
rs58980582	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs60608708	0.84[EUR][1000 genomes]
rs6451666	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6451670	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs673855	0.93[AFR][1000 genomes]
rs6858989	0.92[EUR][1000 genomes]
rs6886503	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7709521	0.88[AFR][1000 genomes]
rs7728625	0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9292865	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv993554	chr5:42720939-43251863	Bivalent/Poised TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	298 gene(s)	inside rSNPs	diseases
2	nsv462126	chr5:42728831-43237188	Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
3	nsv597925	chr5:42728831-43237188	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
4	nsv1023741	chr5:42768215-43348145	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
5	nsv537737	chr5:42768215-43348145	Genic enhancers Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
6	nsv1024636	chr5:42959979-43295782	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
7	nsv537739	chr5:42959979-43295782	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
8	nsv870299	chr5:43053679-43107880	Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43068000-43077600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr5:43068200-43074200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr5:43068600-43082600	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr5:43069000-43081400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr5:43069200-43074200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr5:43069400-43072200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr5:43069400-43075800	Strong transcription	Fetal Stomach	stomach
8	chr5:43069400-43082800	Weak transcription	Colonic Mucosa	Colon
9	chr5:43069400-43087400	Weak transcription	Stomach Mucosa	stomach
10	chr5:43069600-43072400	Strong transcription	Primary T cells from cord blood	blood
11	chr5:43069600-43073200	Strong transcription	Placenta	Placenta
12	chr5:43069600-43073400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr5:43069600-43075200	Weak transcription	Fetal Heart	heart
14	chr5:43069600-43077000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr5:43069600-43080400	Strong transcription	Fetal Muscle Trunk	muscle
16	chr5:43069600-43080400	Strong transcription	Fetal Muscle Leg	muscle
17	chr5:43069800-43072000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr5:43069800-43076000	Weak transcription	GM12878-XiMat	blood
19	chr5:43070000-43072200	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr5:43070000-43073400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr5:43070000-43105400	Weak transcription	HSMMtube	muscle
22	chr5:43070200-43072000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr5:43070200-43072400	Strong transcription	Fetal Intestine Large	intestine
24	chr5:43070200-43072400	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr5:43070200-43073000	Strong transcription	HSMM	muscle
26	chr5:43070200-43073400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr5:43070200-43073600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr5:43070200-43077600	Strong transcription	Fetal Intestine Small	intestine
29	chr5:43070400-43072400	Strong transcription	Adipose Nuclei	Adipose
30	chr5:43070400-43072600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr5:43070400-43073400	Strong transcription	Primary B cells from peripheral blood	blood
32	chr5:43070400-43073400	Strong transcription	Brain Germinal Matrix	brain
33	chr5:43070400-43075000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr5:43070400-43075200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr5:43070400-43075600	Genic enhancers	Dnd41	blood
36	chr5:43070600-43072000	Strong transcription	Brain Substantia Nigra	brain
37	chr5:43070600-43072400	Strong transcription	Muscle Satellite Cultured Cells	--
38	chr5:43070600-43072400	Strong transcription	Liver	Liver
39	chr5:43070600-43073400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr5:43070600-43073400	Strong transcription	Thymus	Thymus
41	chr5:43070800-43072000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr5:43070800-43072000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr5:43070800-43072000	Strong transcription	Left Ventricle	heart
44	chr5:43070800-43072400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr5:43070800-43072400	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr5:43070800-43072400	Strong transcription	NHDF-Ad	bronchial
47	chr5:43070800-43073000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr5:43071000-43072400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr5:43071000-43072400	Strong transcription	Osteobl	bone
50	chr5:43071000-43072800	Strong transcription	Primary neutrophils fromperipheralblood	blood

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