Variant report

Variant	rs6590
Chromosome Location	chr11:73373552-73373553
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:73371264..73374255-chr11:73470720..73472543,3	MCF-7	breast:
2	chr11:73371858..73374878-chr11:73470388..73473197,3	MCF-7	breast:
3	chr11:73308527..73310864-chr11:73370877..73373752,3	MCF-7	breast:
4	chr11:73370621..73373782-chr11:73375391..73378489,3	K562	blood:
5	chr11:73371085..73373574-chr11:73587519..73589689,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000181924	Chromatin interaction
ENSG00000252732	Chromatin interaction
ENSG00000054965	Chromatin interaction
ENSG00000175575	Chromatin interaction
ENSG00000256034	Chromatin interaction
ENSG00000175582	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1043234	1.00[CEU][hapmap]
rs10501412	1.00[CEU][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap]
rs10736793	0.82[GIH][hapmap];0.90[JPT][hapmap]
rs10898927	0.81[ASN][1000 genomes]
rs10898928	0.81[ASN][1000 genomes]
rs10898929	0.81[ASN][1000 genomes]
rs11235834	0.90[JPT][hapmap];1.00[YRI][hapmap]
rs11235843	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]
rs11235844	1.00[CEU][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11235850	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11235851	0.81[TSI][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11235852	0.90[AMR][1000 genomes]
rs11235859	0.90[AMR][1000 genomes]
rs11235860	0.90[AMR][1000 genomes]
rs11235864	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs11235907	1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]
rs11235908	1.00[CEU][hapmap]
rs11235920	0.90[CEU][hapmap]
rs11235922	1.00[CEU][hapmap]
rs11235925	1.00[CEU][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap]
rs11235927	1.00[CEU][hapmap]
rs12365080	1.00[CEU][hapmap]
rs12366033	1.00[CEU][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1568895	0.82[ASN][1000 genomes]
rs17132369	1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs1723840	0.90[JPT][hapmap]
rs1869433	1.00[CEU][hapmap]
rs2037710	0.81[AMR][1000 genomes]
rs2140892	0.82[GIH][hapmap];0.90[JPT][hapmap]
rs2272248	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3741147	0.90[GIH][hapmap];0.82[JPT][hapmap];0.95[TSI][hapmap]
rs3825003	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4944028	1.00[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs4944029	0.84[AMR][1000 genomes]
rs4944032	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs4944034	1.00[CEU][hapmap]
rs4944850	0.82[JPT][hapmap]
rs4944852	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4944856	1.00[CEU][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes]
rs6592531	0.82[GIH][hapmap];0.90[JPT][hapmap]
rs66481935	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs66556722	0.90[AMR][1000 genomes]
rs68128239	0.84[AMR][1000 genomes]
rs7119528	1.00[CEU][hapmap]
rs7128512	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs72974833	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72974840	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72974866	0.84[AMR][1000 genomes]
rs72974869	0.81[AMR][1000 genomes]
rs7939193	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap]
rs9666549	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3395161	chr11:73084616-73461577	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv530624	chr11:73114283-73646329	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv492091	chr11:73285970-73844424	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	nsv1045149	chr11:73314565-73581908	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
5	nsv530641	chr11:73358393-73638725	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	nsv521125	chr11:73359236-73378142	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6590	PAAF1	cis	lymphoblastoid	seeQTL

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:73362000-73375000	Weak transcription	Aorta	Aorta
2	chr11:73363800-73385400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr11:73371600-73374200	Strong transcription	HepG2	liver
4	chr11:73372200-73375600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr11:73372400-73374400	Weak transcription	Psoas Muscle	Psoas
6	chr11:73372400-73374800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr11:73372400-73375000	Weak transcription	Left Ventricle	heart
8	chr11:73372400-73388200	Weak transcription	HSMMtube	muscle
9	chr11:73372400-73395400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr11:73372600-73373800	Weak transcription	A549	lung
11	chr11:73372600-73373800	Weak transcription	K562	blood
12	chr11:73372600-73374000	Weak transcription	GM12878-XiMat	blood
13	chr11:73372600-73374200	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr11:73372600-73374400	Strong transcription	Brain Substantia Nigra	brain
15	chr11:73372600-73374600	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr11:73372600-73374600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr11:73372600-73374600	Weak transcription	Right Atrium	heart
18	chr11:73372600-73374800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr11:73372600-73375000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr11:73372600-73375000	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr11:73372600-73375000	Weak transcription	Fetal Kidney	kidney
22	chr11:73372600-73375000	Weak transcription	Lung	lung
23	chr11:73372600-73383000	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr11:73372600-73384800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr11:73372600-73385200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr11:73372600-73385200	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr11:73372600-73385200	Weak transcription	Liver	Liver
28	chr11:73372600-73385200	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr11:73372600-73385400	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr11:73372600-73385600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr11:73372600-73388200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr11:73372600-73388200	Weak transcription	Duodenum Mucosa	Duodenum
33	chr11:73372600-73388400	Weak transcription	Dnd41	blood
34	chr11:73372600-73394800	Weak transcription	Brain Germinal Matrix	brain
35	chr11:73372800-73373600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
36	chr11:73372800-73373600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr11:73372800-73373800	Weak transcription	Adipose Nuclei	Adipose
38	chr11:73372800-73373800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr11:73372800-73373800	Weak transcription	Osteobl	bone
40	chr11:73372800-73374000	Strong transcription	Brain Angular Gyrus	brain
41	chr11:73372800-73374000	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr11:73372800-73374000	Weak transcription	NHDF-Ad	bronchial
43	chr11:73372800-73374400	Weak transcription	Primary T cells from cord blood	blood
44	chr11:73372800-73374400	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr11:73372800-73374400	Weak transcription	Spleen	Spleen
46	chr11:73372800-73374600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr11:73372800-73374600	Strong transcription	Brain Inferior Temporal Lobe	brain
48	chr11:73372800-73374600	Weak transcription	Fetal Muscle Leg	muscle
49	chr11:73372800-73375000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr11:73372800-73375000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links