Variant report

Variant	rs9369055
Chromosome Location	chr6:38361176-38361177
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:38277946..38279644-chr6:38359626..38361266,2	MCF-7	breast:

Extended variants
information (count: 68 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs12208912	0.85[JPT][hapmap]
rs12215330	0.85[JPT][hapmap]
rs1983605	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs2294739	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4140443	1.00[CEU][hapmap];0.87[CHB][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4711538	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4711540	0.86[EUR][1000 genomes]
rs4711541	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4711543	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4711544	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4711546	1.00[CEU][hapmap];0.84[GIH][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes]
rs4714149	0.83[CHB][hapmap]
rs4714151	0.88[EUR][1000 genomes]
rs4714152	0.94[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes]
rs4714153	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4714155	1.00[CEU][hapmap];0.92[CHB][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4714156	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4714157	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs4714158	1.00[CEU][hapmap];0.83[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs58424668	0.87[EUR][1000 genomes]
rs58807047	0.87[EUR][1000 genomes]
rs6903060	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.89[LWK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs6903611	1.00[CEU][hapmap];0.83[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs6903767	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.89[LWK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs6923701	0.95[EUR][1000 genomes]
rs742515	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs7743023	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7748599	1.00[CEU][hapmap];0.84[GIH][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes]
rs7749685	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs7756267	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs7759078	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7759629	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs7764502	1.00[CEU][hapmap];0.83[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs7766214	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs9296248	1.00[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs9296249	1.00[CEU][hapmap];0.94[TSI][hapmap];0.97[EUR][1000 genomes]
rs9349076	0.96[EUR][1000 genomes]
rs9349077	0.94[CEU][hapmap];0.95[EUR][1000 genomes]
rs9349078	0.95[EUR][1000 genomes]
rs9349079	0.95[EUR][1000 genomes]
rs9357269	0.92[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs9357270	0.92[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs9357271	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.81[LWK][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs9357272	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs9366957	0.84[EUR][1000 genomes]
rs9366959	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9366960	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9369057	0.94[CEU][hapmap];0.95[EUR][1000 genomes]
rs9380740	1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9380741	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9380742	1.00[CEU][hapmap];0.83[JPT][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs9380743	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs9380745	0.94[CEU][hapmap];0.84[EUR][1000 genomes]
rs9380747	1.00[CEU][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs9394493	1.00[CEU][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9394494	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9470865	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9470867	1.00[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs9470868	1.00[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs9470874	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv534620	chr6:38049585-38602064	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv885818	chr6:38147745-38436317	Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv885820	chr6:38166511-38468887	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv602957	chr6:38305770-38395874	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv1032358	chr6:38323745-38415855	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv1022724	chr6:38332368-38454527	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9369055	STK38	cis	cerebellum	SCAN
rs9369055	TDRG1	cis	cerebellum	SCAN
rs9369055	GLO1	cis	parietal	SCAN
rs9369055	PACSIN1	cis	cerebellum	SCAN
rs9369055	KCNK5	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38343000-38367800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:38350200-38366200	Weak transcription	Lung	lung
3	chr6:38354000-38376000	Weak transcription	Primary T cells from cord blood	blood
4	chr6:38354800-38370800	Weak transcription	Primary B cells from cord blood	blood
5	chr6:38358400-38361200	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr6:38358800-38361200	Enhancers	iPS-20b Cell Line	embryonic stem cell
7	chr6:38358800-38362200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr6:38358800-38362800	Enhancers	HUVEC	blood vessel
9	chr6:38359600-38361800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr6:38359600-38367200	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr6:38359800-38361200	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr6:38359800-38363800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr6:38359800-38365200	Weak transcription	Fetal Heart	heart
14	chr6:38360000-38361800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr6:38360000-38361800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr6:38360000-38361800	Weak transcription	NHEK	skin
17	chr6:38360000-38372200	Weak transcription	Psoas Muscle	Psoas
18	chr6:38360400-38362000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr6:38360400-38365200	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr6:38360400-38372800	Weak transcription	Left Ventricle	heart
21	chr6:38361000-38361400	Enhancers	HUES64 Cell Line	embryonic stem cell

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