Variant report

Variant	rs1261412
Chromosome Location	chr1:56975842-56975843
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:56970988..56973563-chr1:56974719..56979116,4	K562	blood:
2	chr1:56975566..56978335-chr1:56981711..56983433,2	MCF-7	breast:
3	chr1:56973352..56978913-chr1:56979369..56985140,11	K562	blood:
4	chr1:56975331..56977635-chr1:56982955..56985243,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000162407	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1261413	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1261414	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1319274	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1361823	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17114046	1.00[CHD][hapmap]
rs17407790	1.00[CHB][hapmap]
rs1777276	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2798153	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56198059	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61772594	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9970807	1.00[CHD][hapmap]

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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1261412	DIO1	cis	cerebellum	SCAN
rs1261412	PCSK9	cis	cerebellum	SCAN
rs1261412	PPAP2B	cis	parietal	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:56958000-56977000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:56960800-56976000	Genic enhancers	HepG2	liver
3	chr1:56962400-56976000	Weak transcription	NH-A	brain
4	chr1:56964800-56976000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
5	chr1:56964800-56979200	Genic enhancers	NHDF-Ad	bronchial
6	chr1:56966000-56980600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr1:56967000-57002000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:56967400-56978400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr1:56968000-56976000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
10	chr1:56969000-56979200	Genic enhancers	Lung	lung
11	chr1:56970400-56977400	Genic enhancers	Fetal Intestine Large	intestine
12	chr1:56970800-56977400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
13	chr1:56970800-56978000	Genic enhancers	Fetal Intestine Small	intestine
14	chr1:56970800-56978200	Enhancers	Right Atrium	heart
15	chr1:56971000-56978000	Strong transcription	Thymus	Thymus
16	chr1:56971000-56979200	Genic enhancers	Left Ventricle	heart
17	chr1:56971400-56977000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
18	chr1:56971400-56986200	Genic enhancers	Placenta	Placenta
19	chr1:56971600-56976400	Enhancers	Psoas Muscle	Psoas
20	chr1:56971600-56977200	Genic enhancers	Fetal Thymus	thymus
21	chr1:56971600-56977800	Genic enhancers	Fetal Muscle Leg	muscle
22	chr1:56971600-56978200	Genic enhancers	Right Ventricle	heart
23	chr1:56971600-56978400	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr1:56971600-56979200	Genic enhancers	Adipose Nuclei	Adipose
25	chr1:56972200-56977600	Genic enhancers	NHLF	lung
26	chr1:56972400-56990800	Strong transcription	HSMM	muscle
27	chr1:56972600-56981800	Weak transcription	Primary B cells from peripheral blood	blood
28	chr1:56972800-56976800	Weak transcription	HSMMtube	muscle
29	chr1:56973000-56976800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr1:56973200-56976600	Enhancers	Pancreas	Pancrea
31	chr1:56973200-56977200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr1:56973400-56978600	Weak transcription	HUVEC	blood vessel
33	chr1:56973600-56976000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr1:56973600-56977200	Enhancers	Fetal Heart	heart
35	chr1:56973800-56976000	Enhancers	Liver	Liver
36	chr1:56973800-56977200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr1:56974000-56976000	Weak transcription	Fetal Kidney	kidney
38	chr1:56974000-56976800	Enhancers	Brain Cingulate Gyrus	brain
39	chr1:56974200-56976200	Enhancers	Brain Inferior Temporal Lobe	brain
40	chr1:56974200-56977600	Enhancers	K562	blood
41	chr1:56974200-56977800	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr1:56974200-56978000	Genic enhancers	Brain Anterior Caudate	brain
43	chr1:56974400-56976400	Weak transcription	A549	lung
44	chr1:56974400-56976800	Weak transcription	Rectal Smooth Muscle	rectum
45	chr1:56974600-56976000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr1:56974600-56976600	Enhancers	Duodenum Mucosa	Duodenum
47	chr1:56974600-56982400	Strong transcription	Osteobl	bone
48	chr1:56974800-56976000	Weak transcription	Stomach Mucosa	stomach
49	chr1:56974800-56976000	Enhancers	Spleen	Spleen
50	chr1:56974800-56976200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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