Variant report

Variant	rs9489193
Chromosome Location	chr6:117769728-117769729
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	chr6:117763172..117766100-chr6:117768265..117771221,3	MCF-7	breast:
2	chr6:117769491..117771172-chr6:117894297..117895800,2	K562	blood:

Variant related genes	Relation type
ENSG00000047932	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs13192511	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13193572	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs13195478	0.88[JPT][hapmap]
rs13195673	0.94[JPT][hapmap]
rs13202514	0.84[ASN][1000 genomes]
rs13205986	0.89[JPT][hapmap]
rs13207962	0.83[CHB][hapmap];0.89[JPT][hapmap]
rs13208369	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13210963	0.83[CHB][hapmap];0.88[JPT][hapmap]
rs13211956	0.82[CHB][hapmap];0.93[JPT][hapmap]
rs13212002	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13218378	0.94[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs1407181	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1407182	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17079188	0.91[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs17079281	0.94[CHB][hapmap];0.82[CHD][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs1853146	0.94[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs1853147	0.95[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs1885064	0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2104064	0.94[CHB][hapmap];0.82[CHD][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs2273601	0.83[ASW][hapmap];0.94[JPT][hapmap];0.87[LWK][hapmap];0.84[MKK][hapmap];0.93[YRI][hapmap]
rs3777980	0.94[JPT][hapmap]
rs3777982	0.94[JPT][hapmap]
rs4946254	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs6910338	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6930292	0.94[ASW][hapmap];0.80[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.93[LWK][hapmap];0.89[MEX][hapmap];0.84[TSI][hapmap];0.89[YRI][hapmap];0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6936540	0.88[ASN][1000 genomes]
rs6940327	0.82[ASN][1000 genomes]
rs6941337	0.85[EUR][1000 genomes]
rs6941824	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6942067	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs717969	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs717970	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs722359	0.89[JPT][hapmap]
rs7739294	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7746536	0.89[JPT][hapmap]
rs7749229	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7756187	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7763979	0.89[JPT][hapmap]
rs9481719	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9489152	0.85[JPT][hapmap]
rs9489155	0.81[AFR][1000 genomes]
rs9489157	0.81[AFR][1000 genomes]
rs9489166	0.84[AFR][1000 genomes]
rs9489173	0.88[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9489199	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532050	chr6:117528154-118203005	ZNF genes & repeats Enhancers Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9489193	MCM9	cis	parietal	SCAN
rs9489193	GOPC	cis	parietal	SCAN
rs9489193	DCBLD1	cis	Whole Blood	GTEx
rs9489193	MARCKS	cis	cerebellum	SCAN
rs9489193	FRK	cis	cerebellum	SCAN
rs9489193	DCBLD1	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:117763000-117772200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr6:117767400-117770800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:117767400-117771600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr6:117767800-117771200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr6:117768000-117773400	Enhancers	NHEK	skin
6	chr6:117768200-117773200	Enhancers	Osteobl	bone
7	chr6:117768200-117773600	Enhancers	HMEC	breast
8	chr6:117768600-117770400	Enhancers	Hela-S3	cervix
9	chr6:117768800-117772000	Enhancers	NHLF	lung
10	chr6:117769000-117769800	Bivalent Enhancer	Fetal Lung	lung
11	chr6:117769000-117773200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr6:117769200-117769800	Flanking Active TSS	HSMMtube	muscle
13	chr6:117769200-117770000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
14	chr6:117769200-117770000	Flanking Active TSS	A549	lung
15	chr6:117769200-117770000	Flanking Active TSS	NH-A	brain
16	chr6:117769200-117771000	Enhancers	Stomach Mucosa	stomach
17	chr6:117769200-117771000	Bivalent Enhancer	HUVEC	blood vessel
18	chr6:117769200-117771200	Enhancers	Fetal Stomach	stomach
19	chr6:117769200-117773200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr6:117769400-117769800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr6:117769400-117769800	Flanking Active TSS	NHDF-Ad	bronchial
22	chr6:117769600-117769800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr6:117769600-117770000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr6:117769600-117770800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr6:117769600-117770800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr6:117769600-117770800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr6:117769600-117770800	Weak transcription	Brain Substantia Nigra	brain
28	chr6:117769600-117771000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr6:117769600-117771000	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr6:117769600-117771600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr6:117769600-117773400	Enhancers	HSMM	muscle
32	chr6:117769600-117779400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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