Variant report

Variant	rs1328389
Chromosome Location	chr6:39383115-39383116
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:39380640..39382722-chr6:39382902..39386768,3	MCF-7	breast:
2	chr6:39383095..39385437-chr6:39394619..39397067,2	MCF-7	breast:
3	chr6:39383062..39385072-chr6:39481069..39483184,2	K562	blood:
4	chr6:39382301..39385007-chr6:39393318..39396394,3	MCF-7	breast:
5	chr12:16597455..16598975-chr6:39382652..39384184,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10807207	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10947809	0.95[CHB][hapmap];0.93[CHD][hapmap];0.88[ASN][1000 genomes]
rs10947810	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.92[JPT][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10947811	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[JPT][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1106961	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs12527811	0.95[CHB][hapmap];0.93[CHD][hapmap];0.89[ASN][1000 genomes]
rs1328383	0.85[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.83[GIH][hapmap];0.92[JPT][hapmap];0.96[ASN][1000 genomes]
rs1328388	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1328390	1.00[CEU][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1410484	0.96[YRI][hapmap]
rs1887713	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1999045	1.00[CHB][hapmap];0.92[CHD][hapmap];0.89[ASN][1000 genomes]
rs4142117	0.95[CHB][hapmap];0.90[CHD][hapmap];0.92[JPT][hapmap];0.92[ASN][1000 genomes]
rs4142118	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs4392720	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs4714250	0.94[CHB][hapmap];0.86[ASN][1000 genomes]
rs4714251	0.95[CHB][hapmap];0.90[CHD][hapmap];0.88[ASN][1000 genomes]
rs6458114	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6458115	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6900629	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6908396	0.94[CHB][hapmap];0.92[JPT][hapmap]
rs72850620	0.89[ASN][1000 genomes]
rs7759557	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[ASN][1000 genomes]
rs913473	0.88[YRI][hapmap]
rs9367004	0.94[CHB][hapmap];0.93[CHD][hapmap];0.89[ASN][1000 genomes]
rs9367005	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs9367006	0.95[CHB][hapmap];0.93[CHD][hapmap];0.86[ASN][1000 genomes]
rs9369114	1.00[CHB][hapmap];0.96[CHD][hapmap];0.81[GIH][hapmap];0.92[JPT][hapmap];0.96[ASN][1000 genomes]
rs9380860	0.90[ASN][1000 genomes]
rs9394591	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9462543	0.95[CHB][hapmap];0.93[CHD][hapmap];0.88[ASN][1000 genomes]
rs9471089	0.89[ASN][1000 genomes]
rs9471090	1.00[CHB][hapmap];0.92[JPT][hapmap];0.96[ASN][1000 genomes]
rs9471092	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.97[ASN][1000 genomes]
rs9471097	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9471098	0.94[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[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	nsv830645	chr6:39227601-39408310	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv533806	chr6:39270073-39397337	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv885822	chr6:39327708-39721216	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1328389	LOC221442	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:39379600-39383200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr6:39379600-39383800	Weak transcription	Brain Anterior Caudate	brain
3	chr6:39379800-39383200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr6:39379800-39383800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr6:39379800-39383800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr6:39379800-39383800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr6:39379800-39383800	Weak transcription	Brain Hippocampus Middle	brain
8	chr6:39379800-39383800	Weak transcription	NHDF-Ad	bronchial
9	chr6:39379800-39384000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr6:39380000-39383600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr6:39380000-39383800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr6:39380000-39383800	Weak transcription	Brain Substantia Nigra	brain
13	chr6:39380000-39384000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr6:39380000-39387600	Weak transcription	Brain Angular Gyrus	brain
15	chr6:39380200-39383400	Weak transcription	HMEC	breast
16	chr6:39380200-39383800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr6:39380200-39383800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr6:39380200-39384000	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr6:39381400-39390000	Weak transcription	Aorta	Aorta
20	chr6:39382400-39383400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr6:39382400-39385400	Weak transcription	Fetal Brain Male	brain
22	chr6:39382600-39383800	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr6:39382800-39384000	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr6:39383000-39384200	Enhancers	Rectal Smooth Muscle	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links