Variant report

Variant	rs12686587
Chromosome Location	chr9:109752976-109752977
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:109746566..109748897-chr9:109752166..109756916,4	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs12003150	1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs12005883	1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs12350828	1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs12684556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12685671	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1546484	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs16925955	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16925965	1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs16926035	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16926052	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2417761	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs28633093	0.93[ASN][1000 genomes]
rs3764523	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs57147563	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57466834	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58231792	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58403995	0.97[ASN][1000 genomes]
rs58419285	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58431218	0.94[ASN][1000 genomes]
rs58984661	0.97[ASN][1000 genomes]
rs60354530	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60858521	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6477551	1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs6477552	1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs7031901	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7039109	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs7043419	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs73524922	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73524927	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73524936	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7847708	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7848294	1.00[CEU][hapmap]
rs7848891	1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs7851411	1.00[CEU][hapmap]
rs7860806	1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs7865611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs7874076	1.00[CEU][hapmap]
rs9695567	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869202	chr9:108940763-109811530	Genic enhancers Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv869351	chr9:109593212-110191170	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv831680	chr9:109653596-109848827	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:109728000-109776200	Weak transcription	NHDF-Ad	bronchial
2	chr9:109729400-109758600	Weak transcription	A549	lung
3	chr9:109733000-109759200	Weak transcription	Fetal Heart	heart
4	chr9:109733200-109775200	Weak transcription	Gastric	stomach
5	chr9:109733600-109759800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr9:109734200-109768600	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr9:109734400-109763000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr9:109734400-109763200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr9:109734400-109768800	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr9:109734600-109758000	Strong transcription	H1 Cell Line	embryonic stem cell
11	chr9:109734600-109763000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr9:109734800-109760200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr9:109734800-109762800	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr9:109736800-109777400	Weak transcription	HUVEC	blood vessel
15	chr9:109739400-109764600	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr9:109739600-109768200	Weak transcription	Primary hematopoietic stem cells	blood
17	chr9:109739600-109770000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr9:109739600-109773000	Weak transcription	Dnd41	blood
19	chr9:109740000-109776000	Weak transcription	Psoas Muscle	Psoas
20	chr9:109740200-109772200	Weak transcription	Colonic Mucosa	Colon
21	chr9:109740200-109777200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr9:109741800-109771000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr9:109742200-109756000	Weak transcription	Colon Smooth Muscle	Colon
24	chr9:109743000-109754600	Weak transcription	Spleen	Spleen
25	chr9:109743000-109755800	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr9:109743000-109765000	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr9:109743200-109753600	Weak transcription	HSMM	muscle
28	chr9:109744600-109755400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr9:109746200-109753200	Strong transcription	Fetal Brain Female	brain
30	chr9:109746200-109774600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr9:109746800-109762000	Weak transcription	NHEK	skin
32	chr9:109746800-109764200	Weak transcription	Aorta	Aorta
33	chr9:109746800-109778600	Weak transcription	NHLF	lung
34	chr9:109747000-109765200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr9:109747000-109769600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr9:109747000-109769800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr9:109747000-109772200	Weak transcription	Osteobl	bone
38	chr9:109747200-109772200	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr9:109747400-109764600	Weak transcription	Esophagus	oesophagus
40	chr9:109747400-109771400	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr9:109747400-109771600	Weak transcription	Brain Angular Gyrus	brain
42	chr9:109747600-109754000	Weak transcription	Duodenum Mucosa	Duodenum
43	chr9:109747600-109757000	Weak transcription	HSMMtube	muscle
44	chr9:109747600-109764400	Weak transcription	Fetal Intestine Small	intestine
45	chr9:109747600-109765600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr9:109747600-109769600	Weak transcription	Brain Substantia Nigra	brain
47	chr9:109747800-109765400	Weak transcription	Lung	lung
48	chr9:109747800-109770400	Weak transcription	Brain Hippocampus Middle	brain
49	chr9:109747800-109771200	Weak transcription	Rectal Smooth Muscle	rectum
50	chr9:109748000-109762200	Weak transcription	Fetal Brain Male	brain

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