Variant report

Variant	rs11588279
Chromosome Location	chr1:225613976-225613977
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	JUN	chr1:225611820-225617257	K562	blood:	n/a	chr1:225613227-225613237 chr1:225616567-225616575 chr1:225615250-225615261 chr1:225616568-225616575 chr1:225612971-225612983 chr1:225616565-225616577 chr1:225613226-225613238 chr1:225613227-225613237 chr1:225613228-225613236 chr1:225616567-225616575 chr1:225615989-225615998 chr1:225612930-225612939 chr1:225613227-225613237 chr1:225616648-225616657 chr1:225615862-225615871 chr1:225616566-225616576
2	MAX	chr1:225613853-225616765	NB4	blood:	n/a	chr1:225616368-225616378 chr1:225614720-225614727 chr1:225616566-225616575 chr1:225614718-225614728 chr1:225615632-225615642
3	GATA2	chr1:225613582-225614118	HUVEC	blood vessel:	n/a	chr1:225613711-225613727 chr1:225613708-225613729 chr1:225613711-225613727
4	FOS	chr1:225613669-225614241	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr1:225611871-225615203	K562	blood:	n/a	n/a
6	MXI1	chr1:225613968-225616747	IMR90	lung:	n/a	n/a
7	TEAD4	chr1:225613826-225615416	K562	blood:	n/a	chr1:225614248-225614257
8	POLR2A	chr1:225613030-225616753	K562	blood:	n/a	n/a
9	FOS	chr1:225613662-225614070	MCF10A-Er-Src	breast:	n/a	n/a
10	MYC	chr1:225613049-225615057	MCF10A-Er-Src	breast:	n/a	chr1:225614720-225614727 chr1:225614718-225614728 chr1:225613403-225613413
11	POLR2A	chr1:225613874-225617283	Hela-S3	cervix:	n/a	n/a
12	MXI1	chr1:225609788-225616921	SK-N-SH	brain:	n/a	n/a
13	UBTF	chr1:225613917-225616755	K562	blood:	n/a	n/a
14	SMC3	chr1:225613955-225615196	Hela-S3	cervix:	n/a	n/a
15	TBL1XR1	chr1:225613532-225615014	K562	blood:	n/a	n/a
16	POLR2A	chr1:225613808-225617160	PBDE	blood:	n/a	n/a
17	MYC	chr1:225613726-225617110	K562	blood:	n/a	chr1:225616368-225616378 chr1:225614720-225614727 chr1:225616566-225616575 chr1:225614718-225614728 chr1:225615632-225615642
18	E2F4	chr1:225613679-225614002	MCF10A-Er-Src	breast:	n/a	n/a
19	GTF2F1	chr1:225613892-225614894	Hela-S3	cervix:	n/a	n/a
20	MAZ	chr1:225613873-225616829	K562	blood:	n/a	chr1:225616368-225616378 chr1:225614720-225614727 chr1:225616566-225616575 chr1:225615632-225615642
21	CHD1	chr1:225613919-225614989	GM12878	blood:	n/a	n/a
22	MAX	chr1:225613824-225616666	K562	blood:	n/a	chr1:225616368-225616378 chr1:225614720-225614727 chr1:225616566-225616575 chr1:225614718-225614728 chr1:225615632-225615642
23	WRNIP1	chr1:225613856-225615230	GM12878	blood:	n/a	n/a
24	MYC	chr1:225613674-225616825	K562	blood:	n/a	chr1:225616368-225616378 chr1:225614720-225614727 chr1:225616566-225616575 chr1:225614718-225614728 chr1:225615632-225615642

No.	Distal block	Cell Line	Cell type
1	chr1:225605937..225609657-chr1:225612868..225616965,5	MCF-7	breast:
2	chr1:225604992..225607166-chr1:225612913..225616218,4	MCF-7	breast:
3	chr1:225613325..225614871-chr1:225640956..225643217,2	K562	blood:
4	chr1:225569904..225572339-chr1:225612601..225615493,2	K562	blood:

Variant related genes	Relation type
LBR	TF binding region
ENSG00000143815	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1056607	0.81[CEU][hapmap];0.85[CHD][hapmap];0.83[MEX][hapmap]
rs10799312	0.91[CHB][hapmap]
rs12032961	0.83[CHB][hapmap]
rs12034829	0.83[CHB][hapmap]
rs1340865	0.92[CHB][hapmap];0.80[CHD][hapmap]
rs1340867	0.92[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs1891000	0.83[CHB][hapmap]
rs2066233	1.00[CHB][hapmap];0.91[CHD][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs2185529	0.90[ASN][1000 genomes]
rs3766930	0.92[CHB][hapmap]
rs3893032	0.83[CHB][hapmap]
rs4653636	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs499782	0.91[CHB][hapmap]
rs6426075	0.92[CHB][hapmap]
rs6684787	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6687980	0.89[CEU][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6696038	1.00[CHB][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs7541888	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[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	nsv832714	chr1:225592333-225805396	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11588279	LBR	cis	Artery Tibial	GTEx
rs11588279	C1orf95	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225599800-225614000	Weak transcription	Right Ventricle	heart
2	chr1:225609600-225615200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
3	chr1:225609800-225614200	Enhancers	Small Intestine	intestine
4	chr1:225611200-225614000	Enhancers	Fetal Heart	heart
5	chr1:225611400-225614000	Enhancers	Fetal Muscle Leg	muscle
6	chr1:225611600-225614200	Enhancers	Primary B cells from peripheral blood	blood
7	chr1:225612000-225614000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:225612000-225614000	Enhancers	HSMMtube	muscle
9	chr1:225612000-225614200	Flanking Active TSS	Fetal Brain Female	brain
10	chr1:225612000-225614200	Transcr. at gene 5' and 3'	K562	blood
11	chr1:225612000-225614600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr1:225612000-225614600	Flanking Active TSS	Brain Germinal Matrix	brain
13	chr1:225612000-225615000	Flanking Active TSS	Primary B cells from cord blood	blood
14	chr1:225612000-225615400	Flanking Active TSS	Primary hematopoietic stem cells	blood
15	chr1:225612200-225614000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr1:225612200-225614000	Enhancers	Brain Anterior Caudate	brain
17	chr1:225612200-225614000	Flanking Active TSS	A549	lung
18	chr1:225612200-225614200	Flanking Active TSS	Colon Smooth Muscle	Colon
19	chr1:225612200-225614200	Enhancers	Gastric	stomach
20	chr1:225612200-225614400	Flanking Active TSS	HMEC	breast
21	chr1:225612200-225614600	Flanking Active TSS	Osteobl	bone
22	chr1:225612200-225614800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
23	chr1:225612400-225614000	Enhancers	H1 Cell Line	embryonic stem cell
24	chr1:225612400-225614000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:225612400-225614000	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr1:225612400-225614000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr1:225612400-225614000	Enhancers	Right Atrium	heart
28	chr1:225612400-225614000	Enhancers	Sigmoid Colon	Sigmoid Colon
29	chr1:225612400-225614200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr1:225612400-225614200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr1:225612400-225614200	Enhancers	Brain Substantia Nigra	brain
32	chr1:225612400-225614200	Enhancers	Psoas Muscle	Psoas
33	chr1:225612400-225614200	Flanking Active TSS	GM12878-XiMat	blood
34	chr1:225612400-225614400	Flanking Active TSS	NHEK	skin
35	chr1:225612400-225614600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr1:225612400-225614600	Enhancers	Spleen	Spleen
37	chr1:225612400-225614800	Enhancers	Placenta Amnion	Placenta Amnion
38	chr1:225612400-225614800	Flanking Active TSS	NH-A	brain
39	chr1:225612400-225615000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
40	chr1:225612400-225615200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr1:225612600-225614000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr1:225612600-225614000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr1:225612600-225614000	Flanking Active TSS	Thymus	Thymus
44	chr1:225612600-225614200	Flanking Active TSS	HepG2	liver
45	chr1:225612600-225614200	Flanking Active TSS	NHLF	lung
46	chr1:225612600-225614400	Weak transcription	Aorta	Aorta
47	chr1:225612600-225614600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
48	chr1:225612600-225615200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
49	chr1:225612600-225615200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr1:225612800-225614000	Weak transcription	Placenta	Placenta

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