Variant report

Variant	rs11265452
Chromosome Location	chr1:160594238-160594239
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1055880	0.95[CEU][hapmap]
rs1061217	0.83[CEU][hapmap]
rs11265442	0.84[CEU][hapmap]
rs11583402	0.95[CEU][hapmap]
rs11585738	0.96[CEU][hapmap];0.93[MEX][hapmap];0.82[TSI][hapmap]
rs11590035	0.91[CEU][hapmap]
rs12144628	0.84[CEU][hapmap]
rs12402879	0.84[CEU][hapmap]
rs12728784	0.83[CEU][hapmap]
rs12733256	0.85[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs1394078	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs1503854	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs151607	0.92[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs1572382	0.84[CEU][hapmap]
rs164283	1.00[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs16832283	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17381453	0.96[CEU][hapmap];0.93[MEX][hapmap];0.82[TSI][hapmap]
rs17385337	0.87[CEU][hapmap]
rs17385407	0.96[CEU][hapmap]
rs1809963	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1998651	0.84[CEU][hapmap]
rs2025516	0.81[CEU][hapmap]
rs2025517	0.84[CEU][hapmap]
rs2083128	0.83[CEU][hapmap]
rs2099604	0.91[CEU][hapmap]
rs2753260	0.92[CEU][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs3733264	0.96[CEU][hapmap];0.93[MEX][hapmap];0.82[TSI][hapmap]
rs3733265	0.96[CEU][hapmap];0.93[MEX][hapmap];0.82[TSI][hapmap]
rs3733266	0.96[CEU][hapmap]
rs3753381	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.80[MEX][hapmap];0.86[ASN][1000 genomes]
rs3753383	1.00[CHB][hapmap];0.82[MEX][hapmap]
rs3766385	0.96[CEU][hapmap]
rs3766387	0.91[CEU][hapmap]
rs3766388	0.91[CEU][hapmap]
rs3766389	0.96[CEU][hapmap]
rs3816146	0.88[CEU][hapmap]
rs5002947	0.91[CEU][hapmap]
rs55841347	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56168064	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56367214	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61801565	0.81[EUR][1000 genomes]
rs61801567	0.83[EUR][1000 genomes]
rs6662093	0.84[EUR][1000 genomes]
rs6668760	0.84[CEU][hapmap]
rs6670721	0.91[CEU][hapmap];0.86[MEX][hapmap]
rs6687641	0.83[CEU][hapmap]
rs6692382	0.84[CEU][hapmap]
rs7547054	0.83[CEU][hapmap]
rs7550771	0.92[CEU][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.80[EUR][1000 genomes]
rs912582	0.96[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs977019	0.84[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829614	chr1:160465291-160595000	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv831703	chr1:160496124-160643024	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	esv1822379	chr1:160545332-160831143	Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv831714	chr1:160581168-160776809	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs11265452	LSR	trans	brain	seeQTL
rs11265452	SDHC	cis	brain	seeQTL
rs11265452	KCNJ9	cis	parietal	SCAN
rs11265452	ADAMTS4	cis	parietal	SCAN
rs11265452	LAMB2	trans	brain	seeQTL
rs11265452	NHLH1	cis	cerebellum	SCAN
rs11265452	HTRA3	trans	brain	seeQTL
rs11265452	VANGL2	cis	cerebellum	SCAN
rs11265452	OLFML2B	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160584400-160594600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr1:160585600-160594800	Weak transcription	K562	blood
3	chr1:160587400-160598400	Genic enhancers	Fetal Thymus	thymus
4	chr1:160588800-160598000	Genic enhancers	Thymus	Thymus
5	chr1:160589000-160596600	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr1:160589800-160596200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr1:160589800-160599400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr1:160590800-160598000	Enhancers	Dnd41	blood
9	chr1:160591000-160596000	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
10	chr1:160591400-160594800	Genic enhancers	Primary T cells from cord blood	blood
11	chr1:160591400-160596800	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr1:160591800-160595000	Weak transcription	Spleen	Spleen
13	chr1:160591800-160595200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr1:160591800-160595200	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr1:160591800-160595400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr1:160591800-160596400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:160591800-160605200	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
18	chr1:160592000-160595200	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr1:160592000-160596600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr1:160592200-160595400	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr1:160592400-160595800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
22	chr1:160592600-160595600	Enhancers	Small Intestine	intestine
23	chr1:160592800-160601400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr1:160593600-160594400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr1:160593600-160595000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr1:160593800-160595600	Weak transcription	Duodenum Mucosa	Duodenum
27	chr1:160593800-160598400	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr1:160594000-160594800	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr1:160594000-160595200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr1:160594000-160595400	Enhancers	Primary B cells from peripheral blood	blood
31	chr1:160594000-160596600	Enhancers	Primary T helper naive cells from peripheral blood	blood
32	chr1:160594000-160599400	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr1:160594200-160594400	Active TSS	GM12878-XiMat	blood
34	chr1:160594200-160594600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr1:160594200-160594600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr1:160594200-160595200	Flanking Active TSS	Primary B cells from cord blood	blood
37	chr1:160594200-160595400	Weak transcription	Primary hematopoietic stem cells	blood

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