Variant report

Variant	rs12024388
Chromosome Location	chr1:72253577-72253578
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 83 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10789328	1.00[ASN][1000 genomes]
rs10789330	1.00[ASN][1000 genomes]
rs11209818	0.80[JPT][hapmap]
rs11209837	0.94[ASN][1000 genomes]
rs11209840	0.97[ASN][1000 genomes]
rs11209841	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11209842	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11209844	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs11578097	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs11584866	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1158573	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs11588321	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs12023733	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12023757	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12030035	1.00[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12030511	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap]
rs12031657	1.00[CEU][hapmap];0.90[JPT][hapmap]
rs12031842	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.90[TSI][hapmap]
rs12037107	1.00[CEU][hapmap];0.93[CHB][hapmap];0.80[JPT][hapmap]
rs12039538	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12040327	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.90[TSI][hapmap];0.82[YRI][hapmap]
rs12041607	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap]
rs12043796	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap]
rs12048869	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12078969	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs12731898	1.00[ASN][1000 genomes]
rs1459795	0.97[ASN][1000 genomes]
rs1459796	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1459801	1.00[ASN][1000 genomes]
rs1491198	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1591382	0.90[JPT][hapmap]
rs17091704	1.00[CEU][hapmap];0.93[CHB][hapmap];0.80[JPT][hapmap];1.00[TSI][hapmap]
rs17091710	1.00[CEU][hapmap];0.93[CHB][hapmap]
rs17091758	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1817805	1.00[ASN][1000 genomes]
rs1844788	1.00[ASN][1000 genomes]
rs1870523	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1870524	0.94[ASN][1000 genomes]
rs1870525	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2061495	1.00[ASN][1000 genomes]
rs2125775	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2125776	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2125777	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2169096	1.00[ASN][1000 genomes]
rs4649943	0.90[JPT][hapmap]
rs4649945	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4649947	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4649949	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4649950	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4650121	1.00[ASN][1000 genomes]
rs4650122	1.00[ASN][1000 genomes]
rs482060	0.87[CHB][hapmap];0.80[JPT][hapmap]
rs57227393	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57839383	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59851000	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6424447	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6424448	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6671557	1.00[CEU][hapmap];0.93[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6697370	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6701156	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72944128	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72944129	0.89[EUR][1000 genomes]
rs72944192	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72946013	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72946022	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72946034	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72948021	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7520452	0.95[ASN][1000 genomes]
rs7528030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7531512	1.00[CEU][hapmap];0.89[JPT][hapmap]
rs7541406	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7546909	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9662397	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949599	chr1:71655652-72327802	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv1007250	chr1:71998391-72350683	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv534992	chr1:71998391-72350683	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv948821	chr1:72049987-72477221	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1003446	chr1:72060680-72419918	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv817447	chr1:72098815-72558020	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1008210	chr1:72099161-72374197	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv830181	chr1:72155983-72296578	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv916783	chr1:72196061-72707953	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv1007910	chr1:72247302-72543998	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12024388	CXCL11	trans	brain	seeQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:72240600-72256600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr1:72247000-72254400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr1:72249200-72254000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:72249600-72257000	Weak transcription	Primary hematopoietic stem cells	blood
5	chr1:72251000-72256000	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr1:72251600-72254600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr1:72251600-72254800	Weak transcription	Colon Smooth Muscle	Colon
8	chr1:72252200-72253600	Enhancers	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links