Variant report

Variant	rs9548864
Chromosome Location	chr13:40229134-40229135
allele	A/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	chr13:40229131-40230230	GM12891	blood:	n/a	n/a
2	MXI1	chr13:40229121-40230974	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr13:40229066-40230228	Raji	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:40224809..40226726-chr13:40227987..40229515,2	K562	blood:
2	chr13:40229027..40231888-chr13:40233465..40236904,4	MCF-7	breast:

Variant related genes	Relation type
COG6	TF binding region
ENSG00000133103	Chromatin interaction
ENSG00000216014	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1006635	1.00[AMR][1000 genomes]
rs13378904	1.00[AMR][1000 genomes]
rs17060145	1.00[AMR][1000 genomes]
rs2324340	1.00[AMR][1000 genomes]
rs3000477	1.00[AMR][1000 genomes]
rs3000480	1.00[AMR][1000 genomes]
rs3000484	1.00[AMR][1000 genomes]
rs3000486	1.00[AMR][1000 genomes]
rs3012138	1.00[AMR][1000 genomes]
rs3012148	1.00[AMR][1000 genomes]
rs3012150	1.00[AMR][1000 genomes]
rs4268631	1.00[AMR][1000 genomes]
rs4318086	1.00[AMR][1000 genomes]
rs4324019	1.00[AMR][1000 genomes]
rs4326926	1.00[AMR][1000 genomes]
rs4383025	1.00[AMR][1000 genomes]
rs4488331	1.00[AMR][1000 genomes]
rs4943690	1.00[AMR][1000 genomes]
rs6563741	1.00[AMR][1000 genomes]
rs6563744	1.00[AMR][1000 genomes]
rs7319899	1.00[AMR][1000 genomes]
rs7333700	1.00[AMR][1000 genomes]
rs7336514	1.00[AMR][1000 genomes]
rs7490747	1.00[AMR][1000 genomes]
rs7996170	1.00[AMR][1000 genomes]
rs9315727	1.00[AMR][1000 genomes]
rs9532415	1.00[AMR][1000 genomes]
rs9532418	1.00[AMR][1000 genomes]
rs9532421	1.00[AMR][1000 genomes]
rs9594354	1.00[AMR][1000 genomes]
rs9603614	1.00[AMR][1000 genomes]
rs9805352	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054600	chr13:39801283-40545027	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1054797	chr13:40198744-40618428	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
3	nsv541755	chr13:40198744-40618428	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
4	nsv832586	chr13:40222880-40379063	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:40227400-40229400	Weak transcription	Aorta	Aorta
2	chr13:40228800-40229400	Weak transcription	Thymus	Thymus
3	chr13:40229000-40229200	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr13:40229000-40229200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr13:40229000-40229200	Active TSS	Primary T helper cells PMA-I stimulated	--
6	chr13:40229000-40229200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
7	chr13:40229000-40229200	Enhancers	Primary T killer memory cells from peripheral blood	blood
8	chr13:40229000-40229200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr13:40229000-40229200	Enhancers	Adipose Nuclei	Adipose
10	chr13:40229000-40229200	Enhancers	Brain Cingulate Gyrus	brain
11	chr13:40229000-40229200	Enhancers	Fetal Lung	lung
12	chr13:40229000-40229200	Enhancers	Rectal Smooth Muscle	rectum
13	chr13:40229000-40229200	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr13:40229000-40229200	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr13:40229000-40229200	Enhancers	GM12878-XiMat	blood
16	chr13:40229000-40229200	Enhancers	HepG2	liver
17	chr13:40229000-40229200	Enhancers	K562	blood
18	chr13:40229000-40229200	Enhancers	Monocytes-CD14+_RO01746	blood
19	chr13:40229000-40229200	Enhancers	NHEK	skin
20	chr13:40229000-40229200	Enhancers	NHLF	lung
21	chr13:40229000-40229200	Enhancers	Osteobl	bone
22	chr13:40229000-40229400	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr13:40229000-40230400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links