Variant report

Variant	rs12493124
Chromosome Location	chr3:99615263-99615264
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:99614799..99616981-chr3:99982145..99984761,2	K562	blood:
2	chr3:99614799..99617137-chr3:99982145..99984761,3	K562	blood:
3	chr3:99593619..99595201-chr3:99613248..99616084,2	K562	blood:
4	chr3:99613503..99616492-chr3:99619175..99621373,2	K562	blood:
5	chr3:99595319..99596945-chr3:99612997..99615307,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168386	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10804762	0.86[EUR][1000 genomes]
rs12485299	1.00[CEU][hapmap]
rs12486901	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[TSI][hapmap];0.95[EUR][1000 genomes]
rs12487173	1.00[AFR][1000 genomes]
rs12489030	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[TSI][hapmap];0.95[EUR][1000 genomes]
rs12491153	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12493320	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs1492343	1.00[CEU][hapmap]
rs1610263	0.80[CEU][hapmap]
rs1610265	0.89[CEU][hapmap]
rs1871847	1.00[CEU][hapmap];0.96[GIH][hapmap];0.84[EUR][1000 genomes]
rs35590972	0.84[EUR][1000 genomes]
rs3732444	0.93[EUR][1000 genomes]
rs3921767	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs4536867	0.80[CEU][hapmap]
rs4928152	1.00[AFR][1000 genomes]
rs4928220	1.00[CEU][hapmap]
rs4928222	1.00[CEU][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs55874130	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55881709	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55964918	0.84[EUR][1000 genomes]
rs56140081	1.00[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs56223679	0.93[EUR][1000 genomes]
rs56260910	0.84[EUR][1000 genomes]
rs56335268	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61010376	0.93[EUR][1000 genomes]
rs6789694	1.00[AFR][1000 genomes]
rs6792339	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[TSI][hapmap];0.95[EUR][1000 genomes]
rs6800456	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs73150300	1.00[AFR][1000 genomes]
rs73858966	0.93[EUR][1000 genomes]
rs73859911	0.93[EUR][1000 genomes]
rs7632345	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[EUR][1000 genomes]
rs7635633	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs7635871	0.95[EUR][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	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99600800-99638600	Weak transcription	Left Ventricle	heart
2	chr3:99604600-99648200	Weak transcription	Primary T cells from cord blood	blood
3	chr3:99613000-99616000	Enhancers	Primary B cells from cord blood	blood
4	chr3:99613200-99615400	Enhancers	Primary hematopoietic stem cells	blood
5	chr3:99613200-99615600	Enhancers	Primary B cells from peripheral blood	blood
6	chr3:99613400-99616400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr3:99613600-99616000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr3:99613800-99615600	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr3:99613800-99615600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr3:99613800-99615600	Enhancers	HSMM	muscle
11	chr3:99613800-99615800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr3:99613800-99615800	Enhancers	Placenta Amnion	Placenta Amnion
13	chr3:99613800-99616000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr3:99614200-99615400	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr3:99614200-99615400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
16	chr3:99614200-99615600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr3:99614200-99615800	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr3:99614200-99615800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
19	chr3:99614200-99615800	Enhancers	Osteobl	bone
20	chr3:99614200-99616000	Enhancers	HMEC	breast
21	chr3:99614200-99616200	Enhancers	Brain Germinal Matrix	brain
22	chr3:99614400-99615400	Enhancers	Adipose Nuclei	Adipose
23	chr3:99614400-99615400	Flanking Active TSS	A549	lung
24	chr3:99614400-99615800	Enhancers	Hela-S3	cervix
25	chr3:99614400-99616200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr3:99614400-99616600	Enhancers	HepG2	liver
27	chr3:99614600-99615400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr3:99614600-99615400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
29	chr3:99614600-99615400	Enhancers	HSMMtube	muscle
30	chr3:99614600-99615600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr3:99614600-99615800	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr3:99614600-99615800	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr3:99614600-99616000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr3:99614600-99616000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr3:99614600-99616000	Enhancers	iPS-18 Cell Line	embryonic stem cell
36	chr3:99614800-99615400	Enhancers	H1 Cell Line	embryonic stem cell
37	chr3:99614800-99615600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr3:99614800-99615600	Enhancers	GM12878-XiMat	blood
39	chr3:99614800-99615800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr3:99614800-99619400	Weak transcription	Psoas Muscle	Psoas
41	chr3:99615000-99615400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr3:99615000-99615400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr3:99615000-99615400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr3:99615000-99615400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr3:99615000-99615400	Enhancers	Fetal Stomach	stomach
46	chr3:99615000-99615400	Enhancers	Stomach Mucosa	stomach
47	chr3:99615000-99615400	Flanking Active TSS	HUVEC	blood vessel
48	chr3:99615000-99615400	Flanking Active TSS	NHDF-Ad	bronchial
49	chr3:99615000-99615400	Flanking Active TSS	NHEK	skin
50	chr3:99615000-99615400	Flanking Active TSS	NHLF	lung

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