Variant report

Variant	rs12602670
Chromosome Location	chr17:46104880-46104881
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:46101739..46105145-chr17:46207358..46210173,3	MCF-7	breast:
2	chr17:46101075..46105793-chr17:46203518..46208640,6	MCF-7	breast:
3	chr17:46101220..46105616-chr17:46211133..46214847,5	K562	blood:
4	chr17:46100290..46104941-chr17:46183793..46186470,6	MCF-7	breast:
5	chr17:46102704..46105485-chr17:46150295..46153343,3	MCF-7	breast:
6	chr17:46037650..46039403-chr17:46103003..46105504,2	K562	blood:
7	chr17:46102745..46105471-chr17:46206069..46210163,5	K562	blood:
8	chr17:46103470..46105367-chr17:46151436..46152289,6	MCF-7	breast:
9	chr17:46102966..46105388-chr17:46145641..46147394,2	K562	blood:
10	chr17:46044123..46046243-chr17:46103230..46105369,2	MCF-7	breast:
11	chr17:46102851..46105550-chr17:46199872..46202014,2	MCF-7	breast:
12	chr17:46103422..46105528-chr17:46131002..46133417,2	K562	blood:
13	chr11:62607625..62609532-chr17:46102709..46105025,2	K562	blood:
14	chr17:46101261..46104972-chr17:46659979..46662985,3	K562	blood:
15	chr17:46102851..46105314-chr17:46237154..46238995,2	MCF-7	breast:
16	chr17:46101917..46105138-chr17:46176105..46179935,5	K562	blood:

No data

Variant related genes	Relation type
ENSG00000108465	Chromatin interaction
ENSG00000082641	Chromatin interaction
ENSG00000141293	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000108468	Chromatin interaction
ENSG00000002919	Chromatin interaction
ENSG00000120093	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12051	0.98[ASN][1000 genomes]
rs12600980	0.86[EUR][1000 genomes]
rs12601350	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12602131	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12946143	0.89[EUR][1000 genomes]
rs1473117	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16951519	0.93[EUR][1000 genomes]
rs2023885	0.95[EUR][1000 genomes]
rs2229369	0.95[EUR][1000 genomes]
rs2240119	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2240120	0.95[EUR][1000 genomes]
rs2240121	0.89[EUR][1000 genomes]
rs2285860	0.85[EUR][1000 genomes]
rs2325783	0.95[EUR][1000 genomes]
rs3785737	0.83[EUR][1000 genomes]
rs4995899	0.93[EUR][1000 genomes]
rs55920502	0.93[EUR][1000 genomes]
rs55982711	0.85[EUR][1000 genomes]
rs58554000	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72823519	0.85[EUR][1000 genomes]
rs72823528	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72823532	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72823533	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs757353	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8066049	0.82[EUR][1000 genomes]
rs8071199	0.83[EUR][1000 genomes]
rs978263	0.86[EUR][1000 genomes]
rs9890691	0.83[EUR][1000 genomes]
rs9898218	0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469808	chr17:46049868-46228673	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
2	nsv482897	chr17:46049868-46228673	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12602670	CBX1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46103200-46105600	Enhancers	Pancreas	Pancrea
2	chr17:46103400-46105000	Enhancers	Fetal Muscle Leg	muscle
3	chr17:46103400-46105400	Enhancers	K562	blood
4	chr17:46103600-46105000	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr17:46103600-46110600	Weak transcription	Aorta	Aorta
6	chr17:46103800-46107800	Weak transcription	HUVEC	blood vessel
7	chr17:46104000-46105000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr17:46104200-46113800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr17:46104400-46105000	Enhancers	NHEK	skin
10	chr17:46104400-46105400	Enhancers	Skeletal Muscle Male	skeletal muscle
11	chr17:46104400-46107800	Weak transcription	Adipose Nuclei	Adipose
12	chr17:46104400-46107800	Weak transcription	Brain Germinal Matrix	brain
13	chr17:46104400-46109200	Weak transcription	Left Ventricle	heart
14	chr17:46104400-46109400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr17:46104400-46109600	Weak transcription	Ovary	ovary
16	chr17:46104400-46110600	Weak transcription	Spleen	Spleen
17	chr17:46104400-46111000	Weak transcription	Lung	lung
18	chr17:46104400-46114000	Weak transcription	Liver	Liver
19	chr17:46104400-46114000	Weak transcription	Right Ventricle	heart
20	chr17:46104400-46114200	Weak transcription	Brain Substantia Nigra	brain
21	chr17:46104600-46105000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr17:46104600-46105000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr17:46104600-46105200	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr17:46104600-46106000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr17:46104600-46107200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr17:46104600-46107600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr17:46104600-46107600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr17:46104600-46107600	Weak transcription	Esophagus	oesophagus
29	chr17:46104600-46107800	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr17:46104600-46107800	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr17:46104600-46107800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr17:46104600-46107800	Weak transcription	Colon Smooth Muscle	Colon
33	chr17:46104600-46107800	Weak transcription	NH-A	brain
34	chr17:46104600-46107800	Weak transcription	NHLF	lung
35	chr17:46104600-46107800	Weak transcription	Osteobl	bone
36	chr17:46104600-46109000	Weak transcription	Fetal Stomach	stomach
37	chr17:46104600-46109200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr17:46104600-46109200	Weak transcription	Stomach Smooth Muscle	stomach
39	chr17:46104600-46113800	Weak transcription	HSMM	muscle
40	chr17:46104600-46114000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr17:46104600-46114000	Weak transcription	Brain Hippocampus Middle	brain
42	chr17:46104800-46105200	Genic enhancers	Fetal Muscle Trunk	muscle
43	chr17:46104800-46107800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr17:46104800-46107800	Weak transcription	Hela-S3	cervix
45	chr17:46104800-46107800	Weak transcription	HMEC	breast
46	chr17:46104800-46108000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr17:46104800-46109400	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr17:46104800-46111000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr17:46104800-46113800	Weak transcription	NHDF-Ad	bronchial
50	chr17:46104800-46114000	Weak transcription	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links