Variant report

Variant	rs1326670
Chromosome Location	chr20:15427250-15427251
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:153462091..153462609-chr20:15426696..15427544,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1468888	0.86[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs2104589	0.89[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap]
rs2208134	0.82[LWK][hapmap]
rs2208137	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs380512	0.82[CEU][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap];0.85[ASN][1000 genomes]
rs389269	0.85[YRI][hapmap]
rs394042	0.89[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap]
rs426845	0.89[CEU][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap];0.85[ASN][1000 genomes]
rs433078	0.83[YRI][hapmap]
rs453612	0.82[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap];0.87[ASN][1000 genomes]
rs4814370	0.89[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];0.91[YRI][hapmap]
rs4814371	0.81[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs4814376	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6034183	0.86[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs6034185	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs6034186	0.90[JPT][hapmap]
rs6034188	0.86[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap];0.91[YRI][hapmap]
rs6034191	1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.99[ASN][1000 genomes]
rs6034194	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6043268	0.89[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.91[YRI][hapmap]
rs6043269	0.89[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.91[YRI][hapmap]
rs6043282	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6043283	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6043287	0.95[CHB][hapmap];0.81[JPT][hapmap];0.94[ASN][1000 genomes]
rs6079821	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs6079828	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6079833	0.94[CHB][hapmap];0.94[ASN][1000 genomes]
rs6110606	0.86[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.80[MEX][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs727245	0.89[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs727246	0.85[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs727247	0.86[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs927920	0.85[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs932822	0.86[CHB][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062252	chr20:14964258-15547739	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv544206	chr20:14964258-15547739	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv869328	chr20:15325423-16213898	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv833927	chr20:15362602-15520185	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1326670	MGC44328	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:15426200-15427600	Weak transcription	Fetal Kidney	kidney
2	chr20:15426200-15427800	Enhancers	Small Intestine	intestine
3	chr20:15426200-15428200	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr20:15426200-15428200	Enhancers	HMEC	breast
5	chr20:15426200-15428600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr20:15426400-15427600	Enhancers	Colon Smooth Muscle	Colon
7	chr20:15426400-15427800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr20:15426400-15427800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr20:15426400-15427800	Enhancers	Fetal Intestine Large	intestine
10	chr20:15426400-15428600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr20:15426600-15427400	Enhancers	Fetal Intestine Small	intestine
12	chr20:15426600-15427400	Enhancers	NHEK	skin
13	chr20:15426600-15427600	Weak transcription	Fetal Stomach	stomach
14	chr20:15426600-15427800	Weak transcription	Fetal Muscle Leg	muscle
15	chr20:15426800-15427800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr20:15426800-15427800	Weak transcription	Placenta	Placenta
17	chr20:15426800-15428800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr20:15427000-15427400	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr20:15427000-15427400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
20	chr20:15427000-15428200	Enhancers	Stomach Smooth Muscle	stomach
21	chr20:15427200-15427400	Enhancers	Ovary	ovary
22	chr20:15427200-15427800	Weak transcription	Adipose Nuclei	Adipose
23	chr20:15427200-15427800	Enhancers	Right Atrium	heart
24	chr20:15427200-15428000	Enhancers	Fetal Brain Male	brain
25	chr20:15427200-15428200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links