Variant report

Variant	rs6542069
Chromosome Location	chr2:113392181-113392182
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:113390360..113393063-chr2:113482708..113485504,2	K562	blood:
2	chr2:113390812..113393784-chr2:113396279..113398032,2	MCF-7	breast:
3	chr2:113382212..113385648-chr2:113390770..113393800,3	MCF-7	breast:
4	chr2:113391397..113393329-chr2:113501977..113503565,2	K562	blood:
5	chr2:113389533..113392236-chr2:113492953..113495168,2	K562	blood:
6	chr2:113391817..113395681-chr2:113402206..113404439,3	MCF-7	breast:
7	chr2:113388214..113390218-chr2:113391409..113393753,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000237753	Chromatin interaction
ENSG00000144130	Chromatin interaction
ENSG00000144136	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1061254	0.81[EUR][1000 genomes]
rs12994441	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12996187	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17042199	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3936697	0.81[EUR][1000 genomes]
rs4630766	0.80[EUR][1000 genomes]
rs4849087	0.80[EUR][1000 genomes]
rs4849088	0.80[EUR][1000 genomes]
rs4849089	0.80[EUR][1000 genomes]
rs4849090	0.80[EUR][1000 genomes]
rs4849093	0.81[EUR][1000 genomes]
rs6737094	0.81[EUR][1000 genomes]
rs6751117	0.81[EUR][1000 genomes]
rs7558138	0.80[EUR][1000 genomes]
rs7559775	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs885346	0.80[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	nsv458997	chr2:113313794-113431092	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	nsv582708	chr2:113313794-113431092	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv470480	chr2:113373950-113429752	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv428724	chr2:113376894-113555421	Genic enhancers Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6542069	AC079922.3	cis	Artery Aorta	GTEx
rs6542069	AC079922.3	cis	Artery Tibial	GTEx
rs6542069	AC079922.3	cis	Heart Left Ventricle	GTEx
rs6542069	AC079922.3	cis	Muscle Skeletal	GTEx
rs6542069	AC079922.3	cis	Whole Blood	GTEx
rs6542069	AC079922.3	cis	lung	GTEx

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113384200-113392400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:113385000-113396000	Weak transcription	Colonic Mucosa	Colon
3	chr2:113385000-113402600	Weak transcription	Esophagus	oesophagus
4	chr2:113385800-113401800	Weak transcription	Brain Hippocampus Middle	brain
5	chr2:113388800-113394800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr2:113388800-113398200	Weak transcription	Lung	lung
7	chr2:113389000-113395000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr2:113389000-113395000	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr2:113389200-113394800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr2:113389200-113394800	Enhancers	Fetal Thymus	thymus
11	chr2:113389400-113395000	Enhancers	Primary T cells fromperipheralblood	blood
12	chr2:113389400-113402000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr2:113389600-113393800	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr2:113389600-113394000	Weak transcription	Spleen	Spleen
15	chr2:113389600-113394800	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr2:113389600-113395000	Enhancers	Primary T cells from cord blood	blood
17	chr2:113389600-113402200	Weak transcription	Primary B cells from cord blood	blood
18	chr2:113389800-113392600	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr2:113389800-113392600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr2:113389800-113393600	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr2:113389800-113393800	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr2:113389800-113393800	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr2:113389800-113394000	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr2:113389800-113395200	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr2:113389800-113398400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr2:113389800-113400400	Weak transcription	Fetal Intestine Small	intestine
27	chr2:113390000-113394000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr2:113390000-113396800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr2:113390000-113397200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr2:113390000-113398000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr2:113390600-113393400	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr2:113390600-113394600	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr2:113390800-113397400	Weak transcription	K562	blood
34	chr2:113391200-113392200	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr2:113391200-113392600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr2:113391200-113392600	Enhancers	Placenta Amnion	Placenta Amnion
37	chr2:113391200-113393000	Enhancers	Placenta	Placenta
38	chr2:113391400-113392200	Flanking Bivalent TSS/Enh	HepG2	liver
39	chr2:113391400-113394000	Enhancers	GM12878-XiMat	blood
40	chr2:113391400-113394800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
41	chr2:113391400-113398000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr2:113391600-113392800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr2:113391800-113392200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr2:113391800-113393200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
45	chr2:113391800-113395000	Enhancers	Primary T killer memory cells from peripheral blood	blood
46	chr2:113392000-113392200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
47	chr2:113392000-113392200	Enhancers	Duodenum Mucosa	Duodenum
48	chr2:113392000-113392200	Enhancers	Stomach Smooth Muscle	stomach
49	chr2:113392000-113392400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
50	chr2:113392000-113392400	Enhancers	Primary T regulatory cells fromperipheralblood	blood

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