Variant report

Variant	rs530369
Chromosome Location	chr1:179897264-179897265
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:179896181..179898748-chr1:179905765..179908705,2	MCF-7	breast:
2	chr1:179893782..179897328-chr1:179897862..179901956,4	MCF-7	breast:
3	chr1:179894610..179897527-chr1:179897909..179900887,3	MCF-7	breast:
4	chr1:179894674..179898167-chr1:179921605..179924633,3	K562	blood:
5	chr1:179895869..179898507-chr1:179943673..179945207,2	MCF-7	breast:
6	chr1:179850392..179853084-chr1:179896429..179898499,3	MCF-7	breast:
7	chr1:179894674..179897438-chr1:179921605..179924215,2	K562	blood:

Variant related genes	Relation type
ENSG00000272906	Chromatin interaction
ENSG00000135837	Chromatin interaction
ENSG00000260360	Chromatin interaction
ENSG00000143337	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1148812	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1148815	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12062341	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12062383	0.96[CEU][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1281378	0.92[CEU][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1281408	0.92[CEU][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1281410	0.80[CEU][hapmap]
rs1281411	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1281412	0.86[AMR][1000 genomes]
rs1281413	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1281429	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1281430	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1281432	0.92[CEU][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1298477	0.82[AMR][1000 genomes]
rs1298479	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1300068	0.84[CEU][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2007148	0.92[CEU][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2245425	0.81[CEU][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2249346	0.92[CEU][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2762858	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2777908	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2777909	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2777917	0.86[AMR][1000 genomes]
rs2794582	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2794583	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs474258	0.96[CEU][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs475233	0.96[CEU][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs475434	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs479094	0.81[CEU][hapmap];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs480377	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs480498	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs486906	0.81[EUR][1000 genomes]
rs501300	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs505789	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs505837	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs514421	0.81[CEU][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs518774	0.84[CEU][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs522534	1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs530854	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs531814	0.80[CEU][hapmap]
rs538512	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs539181	0.84[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs547776	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs549650	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs553830	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs555270	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs589780	0.92[CEU][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs598098	0.84[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs599185	0.96[CEU][hapmap];0.84[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs600046	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs600553	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs605807	0.96[CEU][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs609521	0.96[CEU][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs612215	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs644412	1.00[CEU][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]

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	nsv429936	chr1:179790343-180214343	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv429947	chr1:179790518-179925104	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	esv1815608	chr1:179813499-180067988	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv429958	chr1:179814306-179994628	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179887400-179897600	Weak transcription	Aorta	Aorta
2	chr1:179887400-179898600	Weak transcription	Right Ventricle	heart
3	chr1:179887400-179899200	Weak transcription	Small Intestine	intestine
4	chr1:179887400-179900600	Weak transcription	Ovary	ovary
5	chr1:179887400-179901600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr1:179887600-179899400	Weak transcription	K562	blood
7	chr1:179887800-179899400	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr1:179888600-179899400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr1:179888800-179900600	Weak transcription	Adipose Nuclei	Adipose
10	chr1:179889000-179899400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr1:179889200-179899200	Weak transcription	HepG2	liver
12	chr1:179891000-179899200	Weak transcription	HUVEC	blood vessel
13	chr1:179891200-179899400	Weak transcription	GM12878-XiMat	blood
14	chr1:179891400-179899400	Weak transcription	Liver	Liver
15	chr1:179891600-179899600	Weak transcription	Duodenum Mucosa	Duodenum
16	chr1:179896200-179898200	Weak transcription	Hela-S3	cervix
17	chr1:179896200-179898800	Weak transcription	NHLF	lung
18	chr1:179896200-179899400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr1:179896200-179899400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr1:179896200-179900200	Weak transcription	NHEK	skin
21	chr1:179896400-179899200	Weak transcription	Osteobl	bone
22	chr1:179896400-179899400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:179896400-179899400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr1:179896600-179899200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr1:179897200-179897400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr1:179897200-179897400	Enhancers	Esophagus	oesophagus
27	chr1:179897200-179897600	Enhancers	Fetal Intestine Large	intestine
28	chr1:179897200-179897600	Enhancers	Fetal Intestine Small	intestine
29	chr1:179897200-179899800	Enhancers	Stomach Mucosa	stomach

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