Variant report

Variant	rs6540546
Chromosome Location	chr1:209845370-209845371
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	STAT3	chr1:209845344-209845491	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:209844097..209846070-chr1:209847217..209849817,2	K562	blood:
2	chr1:209839113..209843084-chr1:209844641..209848547,5	K562	blood:

Variant related genes	Relation type
G0S2	TF binding region
ENSG00000123689	Chromatin interaction
ENSG00000227591	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10779511	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10779512	0.90[CHB][hapmap];0.87[ASN][1000 genomes]
rs3817870	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4844486	1.00[CEU][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap];0.94[TSI][hapmap];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs932374	1.00[CEU][hapmap];0.90[GIH][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873139	chr1:209828955-210050794	Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6540546	IKBKE	cis	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209831400-209846200	Weak transcription	Right Ventricle	heart
2	chr1:209832400-209846600	Weak transcription	Right Atrium	heart
3	chr1:209841600-209846200	Weak transcription	Fetal Intestine Large	intestine
4	chr1:209842800-209845600	Enhancers	Psoas Muscle	Psoas
5	chr1:209843000-209845800	Enhancers	Primary neutrophils fromperipheralblood	blood
6	chr1:209843400-209848200	Enhancers	HMEC	breast
7	chr1:209843600-209845400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
8	chr1:209843800-209846400	Enhancers	Liver	Liver
9	chr1:209843800-209848200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr1:209844000-209845400	Enhancers	Left Ventricle	heart
11	chr1:209844000-209848200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
12	chr1:209844200-209848200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr1:209844400-209846400	Weak transcription	Duodenum Mucosa	Duodenum
14	chr1:209844400-209846400	Weak transcription	Pancreas	Pancrea
15	chr1:209844400-209847800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr1:209844600-209846200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr1:209844600-209846200	Weak transcription	Small Intestine	intestine
18	chr1:209844600-209846400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr1:209844600-209846400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr1:209844600-209846400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:209844600-209846400	Enhancers	Adipose Nuclei	Adipose
22	chr1:209844600-209846400	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr1:209844600-209847400	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr1:209844800-209846400	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr1:209844800-209847200	Enhancers	Hela-S3	cervix
26	chr1:209845000-209846200	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr1:209845000-209847600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr1:209845200-209845400	Enhancers	Fetal Heart	heart
29	chr1:209845200-209846200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr1:209845200-209846200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr1:209845200-209846200	Weak transcription	NHEK	skin
32	chr1:209845200-209847600	Enhancers	K562	blood
33	chr1:209845200-209848000	Enhancers	Primary T helper cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links