Variant report

Variant	rs17554911
Chromosome Location	chr11:16432694-16432695
allele	A/G
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	EBF1	chr11:16432693-16433071	GM12878	blood:	n/a	chr11:16432910-16432923 chr11:16432912-16432921 chr11:16432912-16432922

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:16431065..16433163-chr11:16435913..16438616,2	K562	blood:

Variant related genes	Relation type
SOX6	TF binding region

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1393928	0.83[CEU][hapmap]
rs16933090	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17470624	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17554301	0.93[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4132853	0.85[AMR][1000 genomes]
rs4256940	0.85[AMR][1000 genomes]
rs4365016	0.82[AMR][1000 genomes]
rs4375406	0.85[AMR][1000 genomes]
rs4573649	0.85[AMR][1000 genomes]
rs4756846	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4756853	0.85[AMR][1000 genomes]
rs4757400	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55820833	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56030154	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56225716	0.85[AMR][1000 genomes]
rs57463944	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72871370	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72871390	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72871402	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72873303	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72873307	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72873319	0.85[AMR][1000 genomes]
rs72873340	0.85[AMR][1000 genomes]
rs72873349	0.85[AMR][1000 genomes]
rs72873376	0.85[AMR][1000 genomes]
rs72873390	0.85[AMR][1000 genomes]
rs72873400	0.82[AMR][1000 genomes]
rs72875203	0.82[AMR][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	nsv529731	chr11:16122782-16468170	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv553566	chr11:16329009-16799044	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv832075	chr11:16391700-16490934	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:16417200-16434200	Weak transcription	Psoas Muscle	Psoas
2	chr11:16427400-16435400	Weak transcription	Brain Germinal Matrix	brain
3	chr11:16427400-16438800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:16427600-16440000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr11:16428000-16438600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr11:16428400-16434200	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr11:16429400-16439200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr11:16430400-16440000	Weak transcription	Left Ventricle	heart
9	chr11:16430800-16434400	Weak transcription	K562	blood
10	chr11:16432000-16432800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr11:16432000-16432800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr11:16432000-16433000	Enhancers	NHEK	skin
13	chr11:16432400-16440400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr11:16432600-16433200	Enhancers	Pancreatic Islets	Pancreatic Islet

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links