Variant report

Variant	rs17240054
Chromosome Location	chr4:55573693-55573694
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:55567098..55569303-chr4:55573075..55575854,2	K562	blood:

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11726190	0.88[CEU][hapmap];0.88[CHB][hapmap];0.92[JPT][hapmap];0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs13135792	0.80[MEX][hapmap]
rs2237017	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2237019	0.89[GIH][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs2237020	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2237021	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2237023	0.89[GIH][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs2282775	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2703461	0.89[GIH][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs2703488	0.89[CHD][hapmap];0.91[GIH][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs2855777	0.89[CHD][hapmap];0.91[GIH][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs28729669	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3020821	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3020825	0.86[GIH][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs3020826	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3020827	0.89[GIH][hapmap];0.81[TSI][hapmap]
rs3111791	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3111795	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3111800	0.89[GIH][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs3134884	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3134885	0.81[EUR][1000 genomes]
rs34332764	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3796772	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56295037	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6810872	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999400	chr4:55143598-55776995	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	esv3367952	chr4:55437113-55724644	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv526344	chr4:55522488-56231119	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv1003338	chr4:55566703-55582342	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv1012346	chr4:55571312-55584101	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases
6	esv275029	chr4:55571761-55582463	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv1010844	chr4:55573693-55587972	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:55545600-55575800	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr4:55555600-55574400	Weak transcription	Fetal Stomach	stomach
3	chr4:55557800-55594000	Weak transcription	Aorta	Aorta
4	chr4:55561000-55606600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr4:55562000-55577200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr4:55562800-55597400	Weak transcription	Fetal Muscle Trunk	muscle
7	chr4:55565000-55574000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr4:55565000-55576000	Weak transcription	Ovary	ovary
9	chr4:55565600-55575000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr4:55565600-55592800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr4:55566200-55589600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr4:55567600-55575400	Weak transcription	Brain Germinal Matrix	brain
13	chr4:55567800-55574200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr4:55567800-55587200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr4:55570400-55578600	Weak transcription	Fetal Brain Male	brain
16	chr4:55571000-55580000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr4:55571200-55575200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr4:55572200-55576000	Weak transcription	Fetal Muscle Leg	muscle
19	chr4:55572600-55574200	Weak transcription	Gastric	stomach
20	chr4:55573200-55574200	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr4:55573200-55575400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr4:55573200-55576200	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr4:55573200-55576600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr4:55573400-55573800	Enhancers	Thymus	Thymus
25	chr4:55573400-55574200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr4:55573400-55574600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr4:55573400-55574600	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr4:55573400-55575000	Strong transcription	NHDF-Ad	bronchial
29	chr4:55573400-55576400	Genic enhancers	Primary hematopoietic stem cells	blood
30	chr4:55573400-55576600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr4:55573600-55573800	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr4:55573600-55575400	Weak transcription	HUVEC	blood vessel
33	chr4:55573600-55575400	Enhancers	Monocytes-CD14+_RO01746	blood
34	chr4:55573600-55576400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr4:55573600-55577400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
36	chr4:55573600-55577400	Enhancers	Fetal Thymus	thymus
37	chr4:55573600-55583200	Weak transcription	Brain Substantia Nigra	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links