Variant report

Variant	rs3927760
Chromosome Location	chr1:57002327-57002328
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	chr1:57001901-57002474	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr1:57002261-57002406	HepG2	liver:	n/a	n/a
3	POLR2A	chr1:56998973-57004163	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
RPL21P23	TF binding region

Extended variants
information (count: 23 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1041602	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1418977	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17416285	0.80[CEU][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[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1777279	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1819750	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[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[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6688009	0.94[CEU][hapmap]
rs9437006	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][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	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

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	chr1:56994400-57002600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr1:56995000-57003400	Strong transcription	Fetal Muscle Trunk	muscle
13	chr1:56995000-57003600	Strong transcription	Osteobl	bone
14	chr1:56995200-57003800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr1:56995600-57004600	Weak transcription	Colon Smooth Muscle	Colon
16	chr1:56995800-57004000	Genic enhancers	HepG2	liver
17	chr1:56996000-57002800	Genic enhancers	HUES64 Cell Line	embryonic stem cell
18	chr1:56996200-57003000	Genic enhancers	H1 Cell Line	embryonic stem cell
19	chr1:56996200-57003000	Genic enhancers	HUES6 Cell Line	embryonic stem cell
20	chr1:56996200-57003000	Genic enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr1:56996600-57004000	Strong transcription	HSMM	muscle
22	chr1:56996600-57005200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr1:56996800-57003000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr1:56997000-57003400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr1:56997200-57002600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr1:56997200-57004600	Genic enhancers	Placenta	Placenta
27	chr1:56997400-57002600	Strong transcription	Lung	lung
28	chr1:56997400-57002800	Strong transcription	Placenta Amnion	Placenta Amnion
29	chr1:56997600-57004400	Genic enhancers	Fetal Muscle Leg	muscle
30	chr1:56997800-57002600	Genic enhancers	Brain Anterior Caudate	brain
31	chr1:56997800-57003600	Genic enhancers	Skeletal Muscle Female	skeletal muscle
32	chr1:56998000-57002800	Genic enhancers	Left Ventricle	heart
33	chr1:56998600-57003800	Strong transcription	Fetal Stomach	stomach
34	chr1:56998800-57002600	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr1:56999000-57002400	Strong transcription	Aorta	Aorta
36	chr1:56999200-57002600	Strong transcription	Duodenum Mucosa	Duodenum
37	chr1:56999400-57002600	Genic enhancers	Brain Substantia Nigra	brain
38	chr1:56999400-57002800	Genic enhancers	Skeletal Muscle Male	skeletal muscle
39	chr1:56999400-57012800	Weak transcription	HSMMtube	muscle
40	chr1:56999600-57002800	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr1:56999800-57002800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr1:56999800-57002800	Strong transcription	Stomach Smooth Muscle	stomach
43	chr1:57000000-57002400	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:57000000-57002800	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr1:57000000-57002800	Enhancers	Fetal Heart	heart
46	chr1:57000000-57003800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr1:57000000-57004200	Enhancers	ES-I3 Cell Line	embryonic stem cell
48	chr1:57000200-57003000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr1:57000200-57005000	Weak transcription	Rectal Smooth Muscle	rectum
50	chr1:57000200-57008200	Weak transcription	Fetal Kidney	kidney

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