Variant report

Variant	rs59815577
Chromosome Location	chr1:209792244-209792245
allele	C/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	chr1:209791275-209792328	Hela-S3	cervix:	n/a	n/a
2	MYC	chr1:209792182-209792413	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr1:209791713-209792262	Hela-S3	cervix:	n/a	n/a
4	REST	chr1:209792161-209792415	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr1:209789528-209798172	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
LAMB3	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10489340	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12073223	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12089972	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12090288	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12403733	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17014889	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17014906	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17014942	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17014955	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17015006	0.82[AMR][1000 genomes]
rs2072937	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2072939	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2072942	0.95[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2076219	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2076222	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2076232	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2076347	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2076348	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2076349	0.82[EUR][1000 genomes]
rs2076350	0.82[EUR][1000 genomes]
rs2076352	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2229465	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2229466	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2235542	0.95[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2236889	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2236890	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2282734	0.95[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2282736	0.95[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2282737	0.95[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs36051870	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs58679997	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60927005	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs714971	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][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	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209777800-209793000	Weak transcription	Ovary	ovary
2	chr1:209777800-209796600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr1:209779600-209793400	Weak transcription	Thymus	Thymus
4	chr1:209781600-209793600	Weak transcription	Esophagus	oesophagus
5	chr1:209781600-209793600	Weak transcription	Fetal Lung	lung
6	chr1:209785400-209792400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr1:209785800-209793600	Strong transcription	Fetal Stomach	stomach
8	chr1:209786200-209796200	Strong transcription	HMEC	breast
9	chr1:209786400-209796200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr1:209786600-209794600	Weak transcription	Pancreas	Pancrea
11	chr1:209786800-209800000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:209787200-209795000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:209787200-209808400	Strong transcription	Placenta Amnion	Placenta Amnion
14	chr1:209787400-209816200	Strong transcription	NHEK	skin
15	chr1:209788000-209793800	Weak transcription	Small Intestine	intestine
16	chr1:209788400-209796000	Enhancers	Psoas Muscle	Psoas
17	chr1:209788600-209792400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr1:209788800-209793200	Enhancers	Fetal Heart	heart
19	chr1:209789000-209802800	Strong transcription	Hela-S3	cervix
20	chr1:209789200-209793400	Enhancers	Left Ventricle	heart
21	chr1:209789200-209794800	Enhancers	Placenta	Placenta
22	chr1:209789200-209795400	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr1:209789200-209795800	Enhancers	Right Atrium	heart
24	chr1:209790200-209797800	Enhancers	Brain Germinal Matrix	brain
25	chr1:209790400-209796000	Enhancers	Right Ventricle	heart
26	chr1:209791000-209793400	Enhancers	Brain Cingulate Gyrus	brain
27	chr1:209791200-209795600	Enhancers	HSMMtube	muscle
28	chr1:209791400-209792400	Genic enhancers	Gastric	stomach
29	chr1:209791400-209792600	Weak transcription	Liver	Liver
30	chr1:209791400-209792800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr1:209791400-209792800	Enhancers	Osteobl	bone
32	chr1:209791400-209793600	Enhancers	Brain Hippocampus Middle	brain
33	chr1:209791400-209793800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr1:209791400-209793800	Enhancers	Brain Angular Gyrus	brain
35	chr1:209791400-209794400	Genic enhancers	Duodenum Mucosa	Duodenum
36	chr1:209791600-209792400	Enhancers	Spleen	Spleen
37	chr1:209791600-209792600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr1:209791600-209792600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr1:209791600-209792800	Genic enhancers	Rectal Mucosa Donor 29	rectum
40	chr1:209791600-209795000	Enhancers	Cortex derived primary cultured neurospheres	brain
41	chr1:209791600-209796000	Genic enhancers	Rectal Mucosa Donor 31	rectum
42	chr1:209791800-209792400	Genic enhancers	Colonic Mucosa	Colon
43	chr1:209791800-209792400	Genic enhancers	Sigmoid Colon	Sigmoid Colon
44	chr1:209791800-209792600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr1:209791800-209792800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr1:209791800-209794000	Enhancers	Brain Substantia Nigra	brain
47	chr1:209791800-209794800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr1:209791800-209794800	Enhancers	Fetal Brain Male	brain
49	chr1:209791800-209795800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
50	chr1:209791800-209796000	Enhancers	Muscle Satellite Cultured Cells	--

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