Variant report

Variant	rs28649694
Chromosome Location	chr8:54437033-54437034
allele	C/G
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	RUNX3	chr8:54436989-54437482	GM12878	blood:	n/a	n/a
2	POU2F2	chr8:54436914-54437661	GM12878	blood:	n/a	n/a
3	POLR2A	chr8:54436348-54437067	U87	brain:	n/a	n/a
4	BCL11A	chr8:54436995-54437423	GM12878	blood:	n/a	n/a
5	POLR2A	chr8:54436101-54437305	U87	brain:	n/a	n/a
6	RUNX3	chr8:54437022-54437485	GM12878	blood:	n/a	n/a
7	PAX5	chr8:54436961-54437464	GM12878	blood:	n/a	n/a
8	TCF12	chr8:54436365-54437035	A549	lung:	n/a	n/a
9	POLR2A	chr8:54436348-54437149	U87	brain:	n/a	n/a
10	POLR2A	chr8:54436065-54437265	U87	brain:	n/a	n/a
11	SP1	chr8:54436463-54437055	A549	lung:	n/a	n/a
12	GATA3	chr8:54436203-54437086	T-47D	breast:	n/a	n/a
13	SPI1	chr8:54436978-54437434	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000237807	TF binding region

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10090582	0.85[AMR][1000 genomes]
rs10093741	0.82[AMR][1000 genomes]
rs10095837	1.00[ASN][1000 genomes]
rs11992458	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13439440	0.97[ASN][1000 genomes]
rs16919245	0.81[ASN][1000 genomes]
rs2376143	1.00[ASN][1000 genomes]
rs28587342	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28664823	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59216865	0.81[ASN][1000 genomes]
rs6473841	0.85[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752674	chr8:54181147-54483747	Flanking Active TSS Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:54433400-54437200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr8:54433800-54437200	Active TSS	Breast Myoepithelial Primary Cells	Breast
3	chr8:54433800-54437400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
4	chr8:54434200-54437600	Active TSS	Duodenum Smooth Muscle	Duodenum
5	chr8:54434400-54437400	Active TSS	Rectal Mucosa Donor 29	rectum
6	chr8:54434600-54437400	Active TSS	Brain Hippocampus Middle	brain
7	chr8:54435000-54437400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr8:54435800-54437200	Flanking Active TSS	NH-A	brain
9	chr8:54436000-54437200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr8:54436000-54437200	Enhancers	Sigmoid Colon	Sigmoid Colon
11	chr8:54436000-54437200	Enhancers	Small Intestine	intestine
12	chr8:54436000-54437200	Flanking Active TSS	NHEK	skin
13	chr8:54436000-54437400	Flanking Active TSS	Adipose Nuclei	Adipose
14	chr8:54436000-54437400	Flanking Active TSS	Duodenum Mucosa	Duodenum
15	chr8:54436200-54437200	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr8:54436200-54437200	Enhancers	Pancreas	Pancrea
17	chr8:54436200-54437200	Active TSS	HSMM	muscle
18	chr8:54436200-54437600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr8:54436400-54437600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr8:54436400-54437600	Active TSS	Stomach Smooth Muscle	stomach
21	chr8:54436400-54441800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr8:54436600-54437200	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr8:54436600-54437200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr8:54436600-54437600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr8:54436800-54437200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr8:54436800-54437200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr8:54436800-54437200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr8:54436800-54437200	Flanking Active TSS	Fetal Heart	heart
29	chr8:54436800-54437200	Enhancers	Fetal Lung	lung
30	chr8:54436800-54437200	Enhancers	Fetal Muscle Leg	muscle
31	chr8:54436800-54437200	Enhancers	A549	lung
32	chr8:54436800-54437200	Enhancers	Dnd41	blood
33	chr8:54436800-54437200	Flanking Active TSS	HSMMtube	muscle
34	chr8:54436800-54437200	Enhancers	HUVEC	blood vessel
35	chr8:54436800-54437400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr8:54436800-54437400	Enhancers	Right Atrium	heart
37	chr8:54436800-54437400	Flanking Active TSS	Osteobl	bone
38	chr8:54436800-54437800	Enhancers	Esophagus	oesophagus
39	chr8:54436800-54437800	Flanking Active TSS	GM12878-XiMat	blood
40	chr8:54437000-54437200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr8:54437000-54437200	Enhancers	Cortex derived primary cultured neurospheres	brain
42	chr8:54437000-54437200	Flanking Active TSS	Brain Anterior Caudate	brain
43	chr8:54437000-54437200	Enhancers	Brain Inferior Temporal Lobe	brain
44	chr8:54437000-54437200	Flanking Active TSS	Brain Substantia Nigra	brain
45	chr8:54437000-54437200	Flanking Active TSS	Colonic Mucosa	Colon
46	chr8:54437000-54437200	Flanking Active TSS	Colon Smooth Muscle	Colon
47	chr8:54437000-54437200	Flanking Active TSS	Lung	lung
48	chr8:54437000-54437200	Active TSS	Rectal Smooth Muscle	rectum
49	chr8:54437000-54437200	Enhancers	Right Ventricle	heart
50	chr8:54437000-54437200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle

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