Variant report

Variant	rs2716107
Chromosome Location	chr1:59353441-59353442
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:59244354..59252225-chr1:59338738..59357283,49	K562	blood:
2	chr1:59242511..59252251-chr1:59329388..59355607,72	K562	blood:
3	chr1:59281044..59283680-chr1:59353136..59355336,2	K562	blood:
4	chr1:59248359..59251694-chr1:59350027..59354536,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000234807	Chromatin interaction
ENSG00000177606	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10789072	0.86[JPT][hapmap]
rs10889121	0.85[JPT][hapmap]
rs12142126	0.82[JPT][hapmap]
rs1536159	0.83[JPT][hapmap]
rs2716105	1.00[CEU][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2716113	0.86[JPT][hapmap]
rs2716120	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2764911	0.80[JPT][hapmap]
rs2764914	0.85[JPT][hapmap]
rs3015311	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3015312	0.81[JPT][hapmap]
rs4528141	0.81[CEU][hapmap];0.85[JPT][hapmap]
rs4912382	0.86[JPT][hapmap]
rs72921515	0.83[EUR][1000 genomes]
rs927743	0.81[CEU][hapmap];0.82[JPT][hapmap]

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	nsv1005354	chr1:59283572-59535812	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv829959	chr1:59340330-59503085	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:59319800-59361400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:59344800-59356000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr1:59346200-59353600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr1:59346200-59353800	Enhancers	Psoas Muscle	Psoas
5	chr1:59346400-59354000	Enhancers	Fetal Intestine Small	intestine
6	chr1:59346600-59354000	Enhancers	Fetal Intestine Large	intestine
7	chr1:59347000-59353800	Enhancers	Lung	lung
8	chr1:59347000-59353800	Enhancers	Right Atrium	heart
9	chr1:59347000-59354800	Enhancers	NHDF-Ad	bronchial
10	chr1:59347200-59353800	Enhancers	Sigmoid Colon	Sigmoid Colon
11	chr1:59347200-59354000	Enhancers	Pancreas	Pancrea
12	chr1:59348000-59360800	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr1:59348200-59353600	Enhancers	Fetal Thymus	thymus
14	chr1:59348600-59353600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr1:59349000-59354400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr1:59349600-59353800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr1:59349800-59353800	Enhancers	Adipose Nuclei	Adipose
18	chr1:59350200-59353800	Enhancers	Primary T cells fromperipheralblood	blood
19	chr1:59350600-59354600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr1:59351000-59360800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr1:59351200-59353600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr1:59351200-59359000	Weak transcription	Brain Substantia Nigra	brain
23	chr1:59351400-59359200	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr1:59351600-59353600	Enhancers	NHLF	lung
25	chr1:59351800-59353600	Enhancers	Fetal Lung	lung
26	chr1:59351800-59360800	Weak transcription	Fetal Heart	heart
27	chr1:59352000-59354400	Weak transcription	HUVEC	blood vessel
28	chr1:59352000-59359000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr1:59352200-59358800	Weak transcription	Colonic Mucosa	Colon
30	chr1:59352200-59359000	Weak transcription	Fetal Muscle Trunk	muscle
31	chr1:59352400-59354600	Weak transcription	HMEC	breast
32	chr1:59352400-59360800	Weak transcription	Brain Angular Gyrus	brain
33	chr1:59352600-59353600	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr1:59352600-59353800	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr1:59352600-59354400	Weak transcription	NH-A	brain
36	chr1:59352600-59355600	Weak transcription	Duodenum Mucosa	Duodenum
37	chr1:59352600-59355600	Weak transcription	Small Intestine	intestine
38	chr1:59352800-59354000	Weak transcription	Stomach Smooth Muscle	stomach
39	chr1:59352800-59354600	Weak transcription	Primary T cells from cord blood	blood
40	chr1:59352800-59354600	Weak transcription	K562	blood
41	chr1:59352800-59355400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr1:59352800-59356200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr1:59352800-59358600	Weak transcription	Gastric	stomach
44	chr1:59352800-59360600	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr1:59353000-59353600	Enhancers	Ovary	ovary
46	chr1:59353000-59354600	Weak transcription	HSMM	muscle
47	chr1:59353000-59355000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr1:59353200-59353800	Enhancers	Left Ventricle	heart
49	chr1:59353200-59354400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr1:59353200-59354400	Weak transcription	HSMMtube	muscle

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