Variant report

Variant	rs10199279
Chromosome Location	chr2:113397104-113397105
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:113388586..113390776-chr2:113395916..113398828,2	MCF-7	breast:
2	chr2:113390812..113393784-chr2:113396279..113398032,2	MCF-7	breast:
3	chr2:113396800..113399610-chr2:113484528..113487337,2	MCF-7	breast:
4	chr2:113396469..113398021-chr2:113429600..113431477,2	K562	blood:

Variant related genes	Relation type
ENSG00000144130	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 11 )

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

rs_ID	r²[population]
rs10177499	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1061254	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10746527	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10779886	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11123144	0.96[EUR][1000 genomes]
rs12994441	0.84[EUR][1000 genomes]
rs12996187	0.84[EUR][1000 genomes]
rs13023311	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17042199	0.81[EUR][1000 genomes]
rs2312699	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34109218	0.90[EUR][1000 genomes]
rs3936697	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4630766	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4848286	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4849087	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4849088	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4849089	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4849090	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4849092	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4849093	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4849094	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4849095	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4849096	0.87[AMR][1000 genomes]
rs4849100	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56092429	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61443276	0.82[EUR][1000 genomes]
rs6737094	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6747638	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6747928	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6751117	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6793	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72948491	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7558138	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7559775	0.84[EUR][1000 genomes]
rs885346	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv1010106	chr2:113394981-113556071	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs10199279	AC079922.3	cis	Adipose Subcutaneous	GTEx
rs10199279	AC079922.3	cis	Nerve Tibial	GTEx
rs10199279	AC079922.3	cis	Heart Left Ventricle	GTEx
rs10199279	AC079922.3	cis	Muscle Skeletal	GTEx
rs10199279	AC079922.3	cis	Esophagus Muscularis	GTEx
rs10199279	AC079922.3	cis	Artery Tibial	GTEx
rs10199279	AC079922.3	cis	lung	GTEx
rs10199279	AC079922.3	cis	Esophagus Mucosa	GTEx
rs10199279	AC079922.3	cis	Artery Aorta	GTEx
rs10199279	AC079922.3	cis	Thyroid	GTEx
rs10199279	AC079922.3	cis	Whole Blood	GTEx

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113385000-113402600	Weak transcription	Esophagus	oesophagus
2	chr2:113385800-113401800	Weak transcription	Brain Hippocampus Middle	brain
3	chr2:113388800-113398200	Weak transcription	Lung	lung
4	chr2:113389400-113402000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr2:113389600-113402200	Weak transcription	Primary B cells from cord blood	blood
6	chr2:113389800-113398400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr2:113389800-113400400	Weak transcription	Fetal Intestine Small	intestine
8	chr2:113390000-113397200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr2:113390000-113398000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr2:113390800-113397400	Weak transcription	K562	blood
11	chr2:113391400-113398000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr2:113392200-113397600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr2:113392600-113397800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr2:113392800-113402000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr2:113394000-113398000	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr2:113394400-113397400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr2:113394400-113402000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr2:113394600-113398400	Weak transcription	Spleen	Spleen
19	chr2:113394600-113398800	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr2:113394600-113402000	Weak transcription	Fetal Muscle Leg	muscle
21	chr2:113394800-113397600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr2:113394800-113397800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr2:113394800-113398000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr2:113394800-113398800	Weak transcription	Fetal Thymus	thymus
25	chr2:113394800-113402000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr2:113395000-113397200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr2:113395000-113398000	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr2:113395000-113400200	Weak transcription	Primary T cells from cord blood	blood
29	chr2:113395000-113401400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr2:113395000-113402000	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr2:113395200-113397800	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr2:113395200-113401800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr2:113395600-113398000	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr2:113395600-113400800	Weak transcription	Liver	Liver
35	chr2:113396200-113398000	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr2:113396200-113398600	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr2:113396800-113397800	Enhancers	Muscle Satellite Cultured Cells	--
38	chr2:113396800-113398000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr2:113396800-113398400	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr2:113396800-113399200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr2:113396800-113400400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr2:113397000-113398000	Weak transcription	Colonic Mucosa	Colon
43	chr2:113397000-113398000	Enhancers	HepG2	liver
44	chr2:113397000-113401800	Enhancers	HMEC	breast

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