Variant report

Variant	rs11265607
Chromosome Location	chr1:154357678-154357679
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	chr1:154356874..154359380-chr1:154375145..154377788,2	K562	blood:

Variant related genes	Relation type
ENSG00000160712	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10218433	0.80[EUR][1000 genomes]
rs1073907	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10908834	0.85[EUR][1000 genomes]
rs10908835	0.94[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.85[ASN][1000 genomes]
rs11265593	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11265606	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11265609	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11576181	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11576193	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11577266	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11580178	0.91[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11582424	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12061599	0.81[EUR][1000 genomes]
rs12127600	0.94[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.85[ASN][1000 genomes]
rs12719998	0.83[EUR][1000 genomes]
rs12738097	0.83[EUR][1000 genomes]
rs1889314	0.86[EUR][1000 genomes]
rs1889315	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34437053	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56211693	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61803410	0.81[EUR][1000 genomes]
rs6427627	0.94[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];0.85[ASN][1000 genomes]
rs6427631	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6657938	0.81[EUR][1000 genomes]
rs6659828	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6661909	0.84[EUR][1000 genomes]
rs6696089	0.81[EUR][1000 genomes]
rs6698130	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7525436	0.85[EUR][1000 genomes]
rs7555891	0.81[EUR][1000 genomes]
rs952146	0.94[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];0.80[ASN][1000 genomes]
rs9651054	0.85[ASN][1000 genomes]
rs9662562	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9724691	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9728585	0.83[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	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
4	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
5	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
6	esv3451054	chr1:154182013-154360141	Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
7	nsv521887	chr1:154236570-154684106	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11265607	S100A5	cis	parietal	SCAN
rs11265607	GATAD2B	cis	parietal	SCAN
rs11265607	TARS2	cis	parietal	SCAN
rs11265607	SHC1	cis	parietal	SCAN
rs11265607	SLC39A1	cis	cerebellum	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154326800-154360800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:154356800-154358200	Enhancers	Primary T cells fromperipheralblood	blood
3	chr1:154357000-154357800	Enhancers	Primary T cells from cord blood	blood
4	chr1:154357000-154358000	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr1:154357200-154357800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
6	chr1:154357200-154357800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
7	chr1:154357200-154357800	Enhancers	Right Ventricle	heart
8	chr1:154357200-154357800	Enhancers	HepG2	liver
9	chr1:154357200-154358000	Enhancers	Liver	Liver
10	chr1:154357200-154358400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
11	chr1:154357200-154358600	Enhancers	Colonic Mucosa	Colon
12	chr1:154357200-154358600	Enhancers	Sigmoid Colon	Sigmoid Colon
13	chr1:154357200-154359400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr1:154357400-154357800	Enhancers	Primary hematopoietic stem cells	blood
15	chr1:154357400-154357800	Enhancers	Monocytes-CD14+_RO01746	blood
16	chr1:154357400-154358400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
17	chr1:154357400-154358400	Enhancers	Esophagus	oesophagus
18	chr1:154357400-154358400	Enhancers	Spleen	Spleen
19	chr1:154357400-154358600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr1:154357400-154358600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:154357400-154358600	Enhancers	Duodenum Mucosa	Duodenum
22	chr1:154357400-154358600	Enhancers	Placenta	Placenta
23	chr1:154357400-154358600	Enhancers	Lung	lung
24	chr1:154357400-154358600	Flanking Active TSS	K562	blood
25	chr1:154357400-154358600	Enhancers	NHEK	skin
26	chr1:154357400-154359200	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr1:154357400-154359600	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr1:154357400-154359600	Enhancers	Primary B cells from peripheral blood	blood
29	chr1:154357400-154359600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
30	chr1:154357400-154359600	Enhancers	Fetal Thymus	thymus
31	chr1:154357600-154357800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr1:154357600-154357800	Enhancers	Right Atrium	heart
33	chr1:154357600-154358000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr1:154357600-154358000	Enhancers	Primary T helper cells PMA-I stimulated	--
35	chr1:154357600-154358400	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr1:154357600-154358400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
37	chr1:154357600-154358400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
38	chr1:154357600-154358400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
39	chr1:154357600-154358400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
40	chr1:154357600-154358400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr1:154357600-154358400	Enhancers	Stomach Mucosa	stomach
42	chr1:154357600-154358600	Enhancers	Primary B cells from cord blood	blood
43	chr1:154357600-154358600	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr1:154357600-154359600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links