Variant report

Variant	rs28809811
Chromosome Location	chr8:59475078-59475079
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	POLR2A	chr8:59475068-59475165	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr8:59475065-59475127	GM12878	blood:	n/a	n/a
3	POLR2A	chr8:59474985-59475086	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr8:59469977-59477578	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr8:59474463-59476762	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr8:59464567..59467546-chr8:59474944..59480287,7	MCF-7	breast:
2	chr8:59463439..59469524-chr8:59469766..59475373,11	MCF-7	breast:
3	chr8:59469692..59471649-chr8:59473194..59476156,2	MCF-7	breast:

Variant related genes	Relation type
SDCBP	TF binding region
ENSG00000137575	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10085973	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10090425	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10090964	0.82[EUR][1000 genomes]
rs10092359	0.85[EUR][1000 genomes]
rs10094910	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10099153	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10099240	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10099912	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10100873	0.88[EUR][1000 genomes]
rs10102709	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10106272	0.82[EUR][1000 genomes]
rs10110065	0.84[EUR][1000 genomes]
rs10110111	0.81[EUR][1000 genomes]
rs10111052	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10111180	0.84[EUR][1000 genomes]
rs10111506	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10113750	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10504256	0.85[AMR][1000 genomes]
rs1050504	0.85[EUR][1000 genomes]
rs11775194	0.84[EUR][1000 genomes]
rs11776003	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11783174	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12335008	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12674568	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12674724	0.82[EUR][1000 genomes]
rs12676593	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12678669	0.86[EUR][1000 genomes]
rs12679938	0.85[EUR][1000 genomes]
rs12680104	0.80[EUR][1000 genomes]
rs12680996	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16923562	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16923564	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs16923594	0.86[EUR][1000 genomes]
rs17263989	0.81[EUR][1000 genomes]
rs17272151	0.81[EUR][1000 genomes]
rs1991359	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2130072	0.81[EUR][1000 genomes]
rs28429491	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28650441	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28656336	0.87[EUR][1000 genomes]
rs28711402	0.86[EUR][1000 genomes]
rs3739327	0.82[EUR][1000 genomes]
rs3808609	0.80[EUR][1000 genomes]
rs4282557	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4400367	0.83[EUR][1000 genomes]
rs4579515	0.85[AMR][1000 genomes]
rs55774738	0.83[EUR][1000 genomes]
rs59979442	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6471729	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6471731	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6981601	0.83[EUR][1000 genomes]
rs6986129	0.83[EUR][1000 genomes]
rs7009248	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7009374	0.83[EUR][1000 genomes]
rs7011095	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7014398	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72647424	0.84[EUR][1000 genomes]
rs72647425	0.83[EUR][1000 genomes]
rs72647434	0.85[EUR][1000 genomes]
rs72647435	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72647437	0.86[EUR][1000 genomes]
rs7817515	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7825996	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7827910	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7843989	0.92[AMR][1000 genomes]
rs9297995	0.82[EUR][1000 genomes]
rs9297997	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9297999	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv890938	chr8:59355053-59809785	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv890939	chr8:59471187-59544413	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:59466800-59479800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr8:59467200-59486000	Weak transcription	Brain Angular Gyrus	brain
3	chr8:59467400-59559400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr8:59467600-59479200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr8:59468000-59475800	Weak transcription	Brain Hippocampus Middle	brain
6	chr8:59468000-59476600	Weak transcription	Duodenum Mucosa	Duodenum
7	chr8:59468000-59479000	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr8:59468000-59479600	Weak transcription	HepG2	liver
9	chr8:59468000-59480000	Weak transcription	Brain Substantia Nigra	brain
10	chr8:59468200-59480000	Weak transcription	Fetal Kidney	kidney
11	chr8:59468400-59475800	Weak transcription	Liver	Liver
12	chr8:59468400-59476200	Weak transcription	HMEC	breast
13	chr8:59469000-59476400	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr8:59469200-59476400	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr8:59469200-59476400	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr8:59469200-59477800	Weak transcription	Hela-S3	cervix
17	chr8:59470200-59476200	Genic enhancers	Primary neutrophils fromperipheralblood	blood
18	chr8:59470400-59476400	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr8:59470600-59475800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr8:59470600-59476200	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr8:59471200-59475600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr8:59471200-59475800	Weak transcription	Psoas Muscle	Psoas
23	chr8:59471200-59478000	Weak transcription	A549	lung
24	chr8:59471400-59475400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr8:59471400-59476200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr8:59471600-59489200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr8:59472000-59476400	Strong transcription	HSMM	muscle
28	chr8:59472600-59475400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr8:59472600-59477600	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr8:59472600-59478600	Weak transcription	K562	blood
31	chr8:59472800-59475200	Strong transcription	Primary B cells from cord blood	blood
32	chr8:59472800-59476200	Weak transcription	Rectal Smooth Muscle	rectum
33	chr8:59472800-59477000	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr8:59472800-59477600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr8:59472800-59478000	Weak transcription	Dnd41	blood
36	chr8:59472800-59479200	Weak transcription	Small Intestine	intestine
37	chr8:59472800-59515800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr8:59473000-59475800	Weak transcription	Colon Smooth Muscle	Colon
39	chr8:59473000-59476200	Weak transcription	Stomach Smooth Muscle	stomach
40	chr8:59473000-59476400	Weak transcription	Pancreas	Pancrea
41	chr8:59473000-59478000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr8:59473000-59478000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr8:59473000-59478000	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr8:59473000-59478000	Weak transcription	NH-A	brain
45	chr8:59473000-59486000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr8:59473000-59489400	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr8:59473000-59493200	Weak transcription	Fetal Heart	heart
48	chr8:59473000-59493400	Weak transcription	Esophagus	oesophagus
49	chr8:59473000-59497400	Weak transcription	Stomach Mucosa	stomach
50	chr8:59473000-59506400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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