Variant report

Variant	rs9532423
Chromosome Location	chr13:40299722-40299723
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:40297835..40300183-chr13:40302269..40304121,2	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs12584772	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3012147	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3012153	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3012154	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4303351	0.82[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs4329796	0.82[AMR][1000 genomes]
rs4346098	0.84[AMR][1000 genomes]
rs4603426	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56322803	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6563745	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6650473	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7329513	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7988187	0.82[AMR][1000 genomes]
rs7989518	0.82[AMR][1000 genomes]
rs7994943	0.83[JPT][hapmap]
rs9315726	0.80[AMR][1000 genomes]
rs9532427	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9532435	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9548882	1.00[YRI][hapmap];0.82[AMR][1000 genomes]
rs9548886	0.82[AMR][1000 genomes]
rs9548889	0.82[AMR][1000 genomes]
rs9548892	0.84[AMR][1000 genomes]
rs9548899	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9548902	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9548903	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9548904	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9548921	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9548923	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9548925	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9576885	0.82[AMR][1000 genomes]
rs9576886	0.82[AMR][1000 genomes]
rs9576888	0.80[AMR][1000 genomes]

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	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
6	nsv471130	chr13:40261945-40350912	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9532423	COG6	cis	multi-tissue	Pritchard
rs9532423	COG6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:40255000-40306000	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr13:40255800-40340200	Weak transcription	Psoas Muscle	Psoas
3	chr13:40257600-40310800	Weak transcription	Brain Germinal Matrix	brain
4	chr13:40262800-40311000	Weak transcription	Aorta	Aorta
5	chr13:40262800-40311000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr13:40263200-40302600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr13:40267600-40341200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr13:40274000-40301600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr13:40274600-40327000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr13:40282400-40310800	Weak transcription	Right Ventricle	heart
11	chr13:40283600-40310400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr13:40283600-40311000	Weak transcription	Gastric	stomach
13	chr13:40284200-40310400	Weak transcription	Fetal Stomach	stomach
14	chr13:40284400-40302200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr13:40285200-40317600	Weak transcription	Small Intestine	intestine
16	chr13:40286200-40332200	Weak transcription	Esophagus	oesophagus
17	chr13:40287000-40303000	Weak transcription	NHLF	lung
18	chr13:40287400-40311000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr13:40287400-40311400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr13:40287400-40313000	Weak transcription	NHEK	skin
21	chr13:40287600-40310800	Weak transcription	HSMMtube	muscle
22	chr13:40290200-40311000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr13:40290600-40328600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr13:40291400-40310800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr13:40292000-40302800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr13:40292000-40302800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr13:40292000-40302800	Weak transcription	Fetal Intestine Small	intestine
28	chr13:40292000-40310400	Weak transcription	Fetal Brain Female	brain
29	chr13:40292000-40313400	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr13:40292200-40300200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr13:40292200-40311400	Weak transcription	Fetal Thymus	thymus
32	chr13:40292400-40300400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr13:40292400-40300400	Weak transcription	Stomach Smooth Muscle	stomach
34	chr13:40292400-40314800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr13:40292600-40310600	Weak transcription	Fetal Muscle Trunk	muscle
36	chr13:40292600-40310800	Weak transcription	Fetal Muscle Leg	muscle
37	chr13:40292800-40303400	Strong transcription	Liver	Liver
38	chr13:40292800-40307200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr13:40293000-40301000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr13:40293000-40340800	Weak transcription	Colon Smooth Muscle	Colon
41	chr13:40293400-40312600	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr13:40293600-40329000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr13:40294200-40300200	Weak transcription	NHDF-Ad	bronchial
44	chr13:40294200-40303000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr13:40294200-40305000	Weak transcription	Left Ventricle	heart
46	chr13:40294200-40339200	Weak transcription	Fetal Brain Male	brain
47	chr13:40294400-40300600	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr13:40294400-40301800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr13:40294400-40304000	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr13:40294600-40300400	Weak transcription	Dnd41	blood

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