Variant report

Variant	rs1418977
Chromosome Location	chr1:57003359-57003360
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	chr1:57003171-57004244	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr1:56998973-57004163	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
RPL21P23	TF binding region

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1041602	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17416285	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17470169	0.94[CEU][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1759753	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1777279	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1819750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3927760	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3927761	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41487448	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61772578	0.96[AMR][1000 genomes]
rs61772592	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61772595	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61772618	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61772620	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61772622	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61772623	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61772625	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61772626	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61772627	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6674131	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6688009	0.89[CEU][hapmap]
rs857131	1.00[CHB][hapmap]
rs9437006	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv869295	chr1:56894955-57656562	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv945965	chr1:57003085-57005467	Enhancers Weak transcription Strong transcription Genic enhancers	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:56987000-57015000	Genic enhancers	NHDF-Ad	bronchial
2	chr1:56990000-57004000	Genic enhancers	Liver	Liver
3	chr1:56992800-57011200	Weak transcription	Stomach Mucosa	stomach
4	chr1:56993000-57004600	Weak transcription	Hela-S3	cervix
5	chr1:56993600-57007800	Weak transcription	Primary B cells from cord blood	blood
6	chr1:56993800-57004200	Weak transcription	NH-A	brain
7	chr1:56994000-57004000	Weak transcription	HUVEC	blood vessel
8	chr1:56994000-57012400	Weak transcription	Fetal Brain Male	brain
9	chr1:56994000-57012800	Weak transcription	Fetal Brain Female	brain
10	chr1:56994200-57004400	Strong transcription	Muscle Satellite Cultured Cells	--
11	chr1:56995000-57003400	Strong transcription	Fetal Muscle Trunk	muscle
12	chr1:56995000-57003600	Strong transcription	Osteobl	bone
13	chr1:56995200-57003800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr1:56995600-57004600	Weak transcription	Colon Smooth Muscle	Colon
15	chr1:56995800-57004000	Genic enhancers	HepG2	liver
16	chr1:56996600-57004000	Strong transcription	HSMM	muscle
17	chr1:56996600-57005200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr1:56997000-57003400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr1:56997200-57004600	Genic enhancers	Placenta	Placenta
20	chr1:56997600-57004400	Genic enhancers	Fetal Muscle Leg	muscle
21	chr1:56997800-57003600	Genic enhancers	Skeletal Muscle Female	skeletal muscle
22	chr1:56998600-57003800	Strong transcription	Fetal Stomach	stomach
23	chr1:56999400-57012800	Weak transcription	HSMMtube	muscle
24	chr1:57000000-57003800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr1:57000000-57004200	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr1:57000200-57005000	Weak transcription	Rectal Smooth Muscle	rectum
27	chr1:57000200-57008200	Weak transcription	Fetal Kidney	kidney
28	chr1:57000400-57004000	Strong transcription	NHLF	lung
29	chr1:57000400-57011000	Weak transcription	Gastric	stomach
30	chr1:57000400-57013000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr1:57000600-57003800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr1:57000600-57005400	Weak transcription	Colonic Mucosa	Colon
33	chr1:57000800-57004000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr1:57001000-57004000	Genic enhancers	Fetal Intestine Large	intestine
35	chr1:57001000-57004200	Enhancers	Pancreas	Pancrea
36	chr1:57001200-57018800	Weak transcription	A549	lung
37	chr1:57001400-57004600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr1:57001800-57003400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr1:57001800-57003400	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr1:57001800-57003600	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr1:57001800-57018600	Weak transcription	Small Intestine	intestine
42	chr1:57001800-57021800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr1:57002000-57004000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr1:57002000-57004000	Enhancers	Fetal Thymus	thymus
45	chr1:57002200-57004400	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr1:57002200-57004400	Enhancers	Psoas Muscle	Psoas
47	chr1:57002400-57003400	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr1:57002400-57003600	Weak transcription	Brain Angular Gyrus	brain
49	chr1:57002400-57004600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:57002400-57005200	Weak transcription	Aorta	Aorta

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