Variant report

Variant	rs11265618
Chromosome Location	chr1:154430092-154430093
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:154429933..154432687-chr1:154440659..154442962,2	K562	blood:
2	chr1:154427927..154430760-chr1:154437313..154439105,2	K562	blood:
3	chr1:154392306..154395112-chr1:154429501..154431445,2	MCF-7	breast:
4	chr1:154424322..154425827-chr1:154428011..154430297,2	K562	blood:
5	chr1:154421013..154422978-chr1:154430070..154432949,2	K562	blood:

Extended variants
information (count: 43 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10159236	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.92[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10752642	1.00[CEU][hapmap];0.84[MEX][hapmap]
rs11265627	1.00[CEU][hapmap];0.84[MEX][hapmap]
rs11804305	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12023358	0.81[ASN][1000 genomes]
rs12047973	0.83[ASN][1000 genomes]
rs12048091	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12048950	0.83[ASN][1000 genomes]
rs14021	1.00[CEU][hapmap];1.00[MEX][hapmap];0.82[EUR][1000 genomes]
rs16836054	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs4288587	1.00[CEU][hapmap]
rs4308966	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4329505	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4345796	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4474240	1.00[CEU][hapmap];0.83[MEX][hapmap]
rs4518898	1.00[CEU][hapmap]
rs4845374	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4845626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4845634	0.80[EUR][1000 genomes]
rs55800510	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55826755	0.85[ASN][1000 genomes]
rs56233546	0.80[EUR][1000 genomes]
rs57502626	0.85[ASN][1000 genomes]
rs61812592	0.85[ASN][1000 genomes]
rs61812593	0.85[ASN][1000 genomes]
rs61812594	0.85[ASN][1000 genomes]
rs61812596	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61812599	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61812626	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61812631	0.80[EUR][1000 genomes]
rs6427716	1.00[CEU][hapmap];0.84[MEX][hapmap]
rs6670375	1.00[CEU][hapmap];0.84[MEX][hapmap]
rs6687112	1.00[CEU][hapmap];0.84[MEX][hapmap]
rs6691727	1.00[CEU][hapmap];0.84[MEX][hapmap]
rs72698167	0.80[EUR][1000 genomes]
rs7513603	1.00[CEU][hapmap];0.84[MEX][hapmap]
rs7539745	1.00[CEU][hapmap]
rs7543174	0.94[CEU][hapmap];0.81[TSI][hapmap]
rs7553602	1.00[CEU][hapmap]
rs9427415	1.00[CEU][hapmap];1.00[MEX][hapmap]

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	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
2	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
3	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11265618	SNX27	cis	parietal	SCAN
rs11265618	CHRNB2	cis	parietal	SCAN
rs11265618	SMCP	cis	parietal	SCAN
rs11265618	RPTN	cis	cerebellum	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154414800-154436000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:154416200-154435800	Strong transcription	Liver	Liver
3	chr1:154418000-154440000	Weak transcription	Small Intestine	intestine
4	chr1:154418600-154432800	Strong transcription	Rectal Mucosa Donor 29	rectum
5	chr1:154419200-154432200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr1:154419200-154435800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr1:154421800-154431800	Strong transcription	Rectal Smooth Muscle	rectum
8	chr1:154422600-154434400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr1:154422600-154437600	Weak transcription	Pancreas	Pancrea
10	chr1:154424800-154436000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr1:154425000-154437200	Weak transcription	Fetal Stomach	stomach
12	chr1:154426000-154434200	Weak transcription	Placenta	Placenta
13	chr1:154426000-154436200	Weak transcription	Brain Cingulate Gyrus	brain
14	chr1:154426200-154431000	Strong transcription	Sigmoid Colon	Sigmoid Colon
15	chr1:154426200-154433600	Strong transcription	Skeletal Muscle Female	skeletal muscle
16	chr1:154426200-154434400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr1:154426200-154436000	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr1:154426400-154432000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr1:154426400-154432800	Strong transcription	Lung	lung
20	chr1:154426400-154434800	Strong transcription	Stomach Smooth Muscle	stomach
21	chr1:154426400-154435600	Weak transcription	Stomach Mucosa	stomach
22	chr1:154426400-154436000	Weak transcription	Esophagus	oesophagus
23	chr1:154426400-154436000	Weak transcription	Fetal Lung	lung
24	chr1:154426400-154438000	Weak transcription	Psoas Muscle	Psoas
25	chr1:154426600-154430200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr1:154426600-154431600	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr1:154426600-154431600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr1:154426600-154431600	Weak transcription	Brain Anterior Caudate	brain
29	chr1:154426600-154432400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr1:154426600-154434800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr1:154426600-154435400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr1:154426600-154435800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr1:154426600-154435800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr1:154426600-154435800	Weak transcription	Fetal Muscle Leg	muscle
35	chr1:154426600-154440600	Weak transcription	Brain Angular Gyrus	brain
36	chr1:154426800-154430600	Strong transcription	Primary T cells from cord blood	blood
37	chr1:154426800-154430800	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr1:154426800-154431400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr1:154426800-154431800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr1:154426800-154431800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr1:154426800-154434400	Weak transcription	Hela-S3	cervix
42	chr1:154426800-154435200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr1:154426800-154435800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr1:154426800-154435800	Weak transcription	Osteobl	bone
45	chr1:154426800-154436000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr1:154426800-154441200	Weak transcription	Brain Substantia Nigra	brain
47	chr1:154426800-154442200	Weak transcription	HepG2	liver
48	chr1:154426800-154450000	Weak transcription	Fetal Intestine Small	intestine
49	chr1:154427000-154431400	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr1:154427000-154431400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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