Variant report

Variant	rs16843935
Chromosome Location	chr1:172123601-172123602
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	chr1:172113447..172116382-chr1:172123052..172125523,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000208024	Chromatin interaction
ENSG00000230630	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10489299	0.92[CHB][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs12562173	1.00[EUR][1000 genomes]
rs12562275	1.00[EUR][1000 genomes]
rs12562403	1.00[EUR][1000 genomes]
rs12564349	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12568723	1.00[EUR][1000 genomes]
rs12568908	1.00[EUR][1000 genomes]
rs12569096	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12569236	1.00[EUR][1000 genomes]
rs12569310	1.00[EUR][1000 genomes]
rs16843801	1.00[EUR][1000 genomes]
rs16843816	1.00[EUR][1000 genomes]
rs16843819	1.00[EUR][1000 genomes]
rs16843820	1.00[EUR][1000 genomes]
rs16843827	1.00[EUR][1000 genomes]
rs16843831	1.00[EUR][1000 genomes]
rs16843837	1.00[EUR][1000 genomes]
rs16843841	1.00[EUR][1000 genomes]
rs16843842	1.00[EUR][1000 genomes]
rs16843915	1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3924561	1.00[EUR][1000 genomes]
rs57417995	0.88[ASN][1000 genomes]
rs59665490	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60255562	0.83[ASN][1000 genomes]
rs73039343	1.00[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532342	chr1:171922237-172133785	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172114400-172137000	Weak transcription	Brain Angular Gyrus	brain
2	chr1:172115000-172133800	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr1:172115600-172132600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr1:172119000-172125000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr1:172122200-172124800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr1:172122200-172124800	Enhancers	HMEC	breast
7	chr1:172122200-172125400	Enhancers	NHEK	skin
8	chr1:172122400-172125000	Weak transcription	Fetal Lung	lung
9	chr1:172123400-172123800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:172123400-172123800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
11	chr1:172123400-172123800	Flanking Active TSS	NHLF	lung
12	chr1:172123400-172124200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr1:172123400-172124400	Enhancers	A549	lung
14	chr1:172123400-172124400	Enhancers	GM12878-XiMat	blood
15	chr1:172123400-172124400	Enhancers	Hela-S3	cervix
16	chr1:172123400-172124600	Enhancers	Primary B cells from cord blood	blood
17	chr1:172123400-172124600	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr1:172123400-172124600	Enhancers	HSMM	muscle
19	chr1:172123400-172124800	Enhancers	Primary B cells from peripheral blood	blood
20	chr1:172123400-172124800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr1:172123400-172124800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr1:172123400-172125200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr1:172123400-172125200	Enhancers	NH-A	brain
24	chr1:172123400-172149200	Weak transcription	Brain Anterior Caudate	brain
25	chr1:172123600-172123800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr1:172123600-172123800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr1:172123600-172123800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr1:172123600-172123800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr1:172123600-172123800	Enhancers	Adipose Nuclei	Adipose
30	chr1:172123600-172124000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr1:172123600-172124000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr1:172123600-172124000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr1:172123600-172124000	Enhancers	Fetal Heart	heart
34	chr1:172123600-172124000	Enhancers	Fetal Kidney	kidney
35	chr1:172123600-172124000	Active TSS	Ovary	ovary
36	chr1:172123600-172124000	Flanking Active TSS	NHDF-Ad	bronchial
37	chr1:172123600-172124200	Flanking Active TSS	HUVEC	blood vessel
38	chr1:172123600-172124200	Flanking Active TSS	Osteobl	bone
39	chr1:172123600-172124400	Enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr1:172123600-172124400	Enhancers	Primary T killer memory cells from peripheral blood	blood
41	chr1:172123600-172124400	Enhancers	HSMMtube	muscle
42	chr1:172123600-172124600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr1:172123600-172124600	Enhancers	Primary T regulatory cells fromperipheralblood	blood

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