Variant report

Variant	rs9532432
Chromosome Location	chr13:40352602-40352603
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:40350876..40353001-chr13:41230658..41232496,2	MCF-7	breast:
2	chr13:40351756..40352604-chr13:41257334..41257872,2	MCF-7	breast:
3	chr13:40351688..40352941-chr13:40516694..40517645,4	MCF-7	breast:
4	chr13:40352027..40354218-chr13:40364182..40366415,2	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11147769	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17591231	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17591266	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4245396	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4338665	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4403927	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4408422	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4409964	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4943694	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4943695	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4943696	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7319128	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7325068	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7327824	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7334651	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7337585	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7998641	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8181861	0.81[AMR][1000 genomes]
rs9315729	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9315730	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9532429	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9532433	0.81[AFR][1000 genomes]
rs9532434	0.80[AFR][1000 genomes]
rs9532436	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9532439	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9548900	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9548901	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9548916	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9548917	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9548918	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9548919	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9548920	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9548926	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9548927	0.80[AMR][1000 genomes]
rs9548928	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9548929	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9548930	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9548932	0.81[AFR][1000 genomes]
rs9566474	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9576891	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9576892	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9576896	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9576897	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9576898	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054600	chr13:39801283-40545027	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1054797	chr13:40198744-40618428	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
3	nsv541755	chr13:40198744-40618428	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
4	nsv832586	chr13:40222880-40379063	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1040458	chr13:40249387-40638129	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9532432	COG6	Cis_1M	lymphoblastoid	RTeQTL
rs9532432	COG6	cis	Muscle Skeletal	GTEx

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:40340400-40353600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr13:40340400-40361200	Weak transcription	Pancreas	Pancrea
3	chr13:40341800-40356600	Weak transcription	Rectal Smooth Muscle	rectum
4	chr13:40342600-40360200	Weak transcription	Fetal Muscle Leg	muscle
5	chr13:40345400-40354800	Weak transcription	Brain Anterior Caudate	brain
6	chr13:40347800-40355200	Enhancers	HUVEC	blood vessel
7	chr13:40350200-40354400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
8	chr13:40350200-40357200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr13:40350800-40354000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr13:40351000-40354400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr13:40351200-40354000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr13:40351200-40354200	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr13:40351400-40353200	Enhancers	NH-A	brain
14	chr13:40351600-40352800	Weak transcription	Psoas Muscle	Psoas
15	chr13:40351600-40352800	Enhancers	Osteobl	bone
16	chr13:40351600-40353400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr13:40351600-40354600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr13:40351800-40352800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr13:40351800-40352800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr13:40351800-40353400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr13:40351800-40354400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr13:40351800-40354400	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr13:40351800-40354600	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr13:40351800-40358400	Weak transcription	Ovary	ovary
25	chr13:40351800-40360200	Weak transcription	Left Ventricle	heart
26	chr13:40352000-40353400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr13:40352000-40353400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr13:40352000-40354400	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr13:40352000-40354600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr13:40352000-40361400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr13:40352200-40353400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr13:40352200-40353400	Weak transcription	HSMMtube	muscle
33	chr13:40352200-40353400	Weak transcription	NHDF-Ad	bronchial
34	chr13:40352200-40353600	Weak transcription	NHLF	lung
35	chr13:40352200-40353800	Weak transcription	Right Atrium	heart
36	chr13:40352200-40354400	Enhancers	Primary T cells from cord blood	blood
37	chr13:40352400-40353200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr13:40352400-40353400	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr13:40352400-40353400	Weak transcription	HMEC	breast
40	chr13:40352400-40353600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr13:40352400-40354400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
42	chr13:40352400-40354400	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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