Variant report

Variant	rs1479355
Chromosome Location	chr6:160530626-160530627
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	chr6:160524963..160527008-chr6:160529525..160532006,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC22A1-2	chr6:160529406-160532536	ENSG00000270949.1

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1867351	1.00[CEU][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2297369	0.86[ASN][1000 genomes]
rs2297370	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs2297371	1.00[CEU][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs2297372	0.85[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.86[ASN][1000 genomes]
rs3798173	1.00[CEU][hapmap];0.90[TSI][hapmap]
rs3822841	1.00[CEU][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap]
rs4646272	0.90[ASN][1000 genomes]
rs4709399	0.83[CEU][hapmap];0.83[ASN][1000 genomes]
rs4709400	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58458113	0.88[EUR][1000 genomes]
rs6900842	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6935207	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs755884	0.84[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs7746102	0.81[ASW][hapmap];0.86[MEX][hapmap]
rs7753051	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7760552	0.81[ASW][hapmap];0.80[CEU][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap]
rs7769472	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9346808	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9347385	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9355776	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9365131	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9365132	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9365133	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758089	chr6:160372244-161234665	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	esv2759484	chr6:160372244-161234665	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	esv35098	chr6:160422589-161070870	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	esv2757197	chr6:160432331-161070870	Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv818463	chr6:160435569-161025547	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1479355	SLC22A1	cis	Whole Blood	GTEx
rs1479355	OSTCL	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:160453000-160534600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr6:160455800-160532000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr6:160464600-160531800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr6:160465600-160530800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr6:160477200-160531200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr6:160477200-160531400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:160487600-160530800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr6:160490200-160531400	Strong transcription	Dnd41	blood
9	chr6:160491200-160531400	Strong transcription	Fetal Thymus	thymus
10	chr6:160510200-160531000	Strong transcription	Muscle Satellite Cultured Cells	--
11	chr6:160511000-160531600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr6:160511000-160531600	Strong transcription	Fetal Muscle Leg	muscle
13	chr6:160511400-160532600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr6:160512000-160532800	Weak transcription	A549	lung
15	chr6:160512000-160539200	Weak transcription	Stomach Mucosa	stomach
16	chr6:160518000-160532200	Weak transcription	Fetal Brain Male	brain
17	chr6:160521800-160537600	Strong transcription	Fetal Intestine Small	intestine
18	chr6:160522000-160531000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr6:160522000-160531400	Strong transcription	Fetal Muscle Trunk	muscle
20	chr6:160522000-160531600	Strong transcription	Thymus	Thymus
21	chr6:160522200-160531400	Strong transcription	Fetal Stomach	stomach
22	chr6:160522400-160531400	Strong transcription	Sigmoid Colon	Sigmoid Colon
23	chr6:160522400-160532000	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr6:160522600-160531400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr6:160522800-160531400	Strong transcription	NHLF	lung
26	chr6:160522800-160532200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr6:160523200-160540200	Weak transcription	Fetal Heart	heart
28	chr6:160525000-160531200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr6:160525800-160531200	Weak transcription	Fetal Kidney	kidney
30	chr6:160526200-160539000	Weak transcription	Colon Smooth Muscle	Colon
31	chr6:160526200-160548600	Weak transcription	K562	blood
32	chr6:160526400-160533400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr6:160526400-160536800	Weak transcription	Primary B cells from peripheral blood	blood
34	chr6:160526800-160531800	Weak transcription	Hela-S3	cervix
35	chr6:160526800-160532000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr6:160526800-160532600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr6:160526800-160532800	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr6:160526800-160532800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr6:160526800-160533000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr6:160526800-160533000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr6:160526800-160533000	Weak transcription	Fetal Brain Female	brain
42	chr6:160526800-160537000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr6:160526800-160538600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr6:160526800-160540600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr6:160526800-160545000	Weak transcription	HMEC	breast
46	chr6:160527000-160532000	Weak transcription	Brain Germinal Matrix	brain
47	chr6:160527000-160532600	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr6:160527000-160532800	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr6:160527000-160538800	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr6:160527000-160545000	Weak transcription	NHDF-Ad	bronchial

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