Variant report

Variant	rs11564122
Chromosome Location	chr12:40547750-40547751
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	12:40545640-40549031..12:40691796-40694737	GM12878	blood:
2	chr12:40158520..40159448-chr12:40546284..40547792,5	MCF-7	breast:
3	12:40545640-40549031..12:40703633-40711447	GM12878	blood:

Variant related genes	Relation type
ENSG00000188906	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10747955	1.00[ASN][1000 genomes]
rs10747959	1.00[ASN][1000 genomes]
rs10784283	1.00[ASN][1000 genomes]
rs10878226	1.00[YRI][hapmap]
rs10878246	1.00[YRI][hapmap]
rs11175620	1.00[YRI][hapmap]
rs11175645	1.00[YRI][hapmap]
rs11175655	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs11175658	1.00[YRI][hapmap]
rs11175666	1.00[YRI][hapmap]
rs11564118	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11564120	1.00[ASN][1000 genomes]
rs11564132	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11564226	1.00[ASN][1000 genomes]
rs11564274	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11564275	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11564277	1.00[MEX][hapmap]
rs12099949	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1497046	1.00[ASN][1000 genomes]
rs1497048	1.00[ASN][1000 genomes]
rs1566127	1.00[ASN][1000 genomes]
rs17442665	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17442735	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17442812	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17442853	1.00[YRI][hapmap]
rs17458341	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17458780	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17458836	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17458974	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17465428	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17489985	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17519573	1.00[YRI][hapmap]
rs2132745	1.00[ASN][1000 genomes]
rs2132746	1.00[ASN][1000 genomes]
rs2404351	1.00[ASN][1000 genomes]
rs28370599	1.00[ASN][1000 genomes]
rs2952711	0.86[EUR][1000 genomes]
rs34714539	1.00[ASN][1000 genomes]
rs35985096	1.00[ASN][1000 genomes]
rs4768196	1.00[ASN][1000 genomes]
rs4768202	1.00[ASN][1000 genomes]
rs6581438	1.00[ASN][1000 genomes]
rs6581439	1.00[ASN][1000 genomes]
rs7135678	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.85[TSI][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7138075	1.00[ASN][1000 genomes]
rs7138078	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs71449744	1.00[ASN][1000 genomes]
rs7294619	1.00[YRI][hapmap]
rs7300161	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7305155	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7305994	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74088117	1.00[ASN][1000 genomes]
rs7959787	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs937385	1.00[ASN][1000 genomes]

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	nsv558596	chr12:40413698-40591117	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv899030	chr12:40509341-40580440	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv899031	chr12:40520684-40580440	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1045516	chr12:40543200-40589557	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40546600-40547800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr12:40546600-40547800	Enhancers	A549	lung
3	chr12:40546600-40548400	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr12:40546800-40548400	Enhancers	Primary neutrophils fromperipheralblood	blood
5	chr12:40547000-40547800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr12:40547000-40547800	Enhancers	Primary B cells from peripheral blood	blood
7	chr12:40547000-40548000	Enhancers	Primary B cells from cord blood	blood
8	chr12:40547200-40547800	Enhancers	HMEC	breast
9	chr12:40547200-40548000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
10	chr12:40547200-40558600	Weak transcription	Liver	Liver
11	chr12:40547400-40547800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr12:40547400-40547800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr12:40547400-40547800	Enhancers	GM12878-XiMat	blood
14	chr12:40547400-40548400	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr12:40547400-40548600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr12:40547600-40551800	Weak transcription	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links