Variant report

Variant	rs12349178
Chromosome Location	chr9:100476352-100476353
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:100475511..100477601-chr9:100564696..100566585,2	MCF-7	breast:
2	chr9:100473102..100474630-chr9:100476302..100477871,2	K562	blood:
3	chr9:100475762..100478483-chr9:100478575..100480618,2	K562	blood:
4	chr9:100475449..100479903-chr9:100484059..100486391,3	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10116536	0.96[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10119687	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs10120102	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10123969	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10983405	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10983424	1.00[EUR][1000 genomes]
rs10983428	1.00[EUR][1000 genomes]
rs12344605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12346336	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12347253	0.99[EUR][1000 genomes]
rs12350221	1.00[EUR][1000 genomes]
rs12350946	1.00[EUR][1000 genomes]
rs16923269	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs16923677	0.96[CEU][hapmap];0.95[EUR][1000 genomes]
rs16923719	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16923815	0.98[EUR][1000 genomes]
rs17335265	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs28376250	0.95[EUR][1000 genomes]
rs3176639	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3176748	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4284139	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4480232	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs4617277	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61047578	0.99[EUR][1000 genomes]
rs7031623	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs72751548	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7849509	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs952765	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893610	chr9:100324086-100496160	Active TSS Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1043753	chr9:100458109-100599265	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100467200-100476400	Weak transcription	Fetal Intestine Large	intestine
2	chr9:100468000-100476600	Weak transcription	GM12878-XiMat	blood
3	chr9:100471200-100476400	Weak transcription	Fetal Intestine Small	intestine
4	chr9:100472800-100476400	Weak transcription	HepG2	liver
5	chr9:100473600-100476400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr9:100473600-100476400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr9:100473600-100476400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr9:100473600-100476600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr9:100473600-100476600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr9:100473800-100476400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr9:100473800-100476400	Weak transcription	NHLF	lung
12	chr9:100473800-100476600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr9:100474000-100476400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr9:100474000-100476400	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr9:100474000-100476600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr9:100474400-100476400	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr9:100475600-100476600	Enhancers	Hela-S3	cervix
18	chr9:100475800-100477400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr9:100475800-100477600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr9:100475800-100477600	Enhancers	HMEC	breast
21	chr9:100475800-100477800	Enhancers	NHEK	skin
22	chr9:100476000-100477200	Enhancers	Muscle Satellite Cultured Cells	--
23	chr9:100476000-100477200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr9:100476000-100477200	Enhancers	Placenta Amnion	Placenta Amnion
25	chr9:100476000-100477200	Enhancers	HSMM	muscle
26	chr9:100476000-100477200	Enhancers	HSMMtube	muscle
27	chr9:100476000-100477200	Enhancers	Osteobl	bone
28	chr9:100476000-100477600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr9:100476200-100476600	Enhancers	Primary T cells from cord blood	blood
30	chr9:100476200-100477000	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr9:100476200-100477000	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr9:100476200-100477000	Flanking Active TSS	A549	lung
33	chr9:100476200-100477200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr9:100476200-100477200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chr9:100476200-100477200	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr9:100476200-100477200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
37	chr9:100476200-100477200	Enhancers	Primary T killer memory cells from peripheral blood	blood
38	chr9:100476200-100477800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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