Variant report

Variant	rs3000491
Chromosome Location	chr10:25239383-25239384
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:25010748..25013945-chr10:25238648..25242767,8	MCF-7	breast:
2	chr10:25010212..25016288-chr10:25239162..25243925,7	K562	blood:
3	chr10:25009082..25014020-chr10:25238727..25242865,5	K562	blood:

Variant related genes	Relation type
ENSG00000107863	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10741072	0.83[ASN][1000 genomes]
rs10828728	0.86[ASN][1000 genomes]
rs10828731	0.88[ASN][1000 genomes]
rs11014318	0.85[ASN][1000 genomes]
rs11014320	0.87[ASN][1000 genomes]
rs12761282	0.81[ASN][1000 genomes]
rs185669	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs200730	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2035888	0.87[ASN][1000 genomes]
rs2478091	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs274297	0.80[ASN][1000 genomes]
rs274299	0.90[ASN][1000 genomes]
rs274300	0.81[ASN][1000 genomes]
rs274301	0.86[ASN][1000 genomes]
rs274303	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs274304	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs274305	0.85[ASN][1000 genomes]
rs274306	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs274307	0.86[ASN][1000 genomes]
rs274308	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs274309	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs274310	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs274311	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs274312	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs274313	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs274316	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3748223	0.83[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053278	chr10:25140776-25269093	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:25191600-25240600	Weak transcription	Stomach Smooth Muscle	stomach
2	chr10:25211400-25239800	Weak transcription	Fetal Kidney	kidney
3	chr10:25215800-25240000	Weak transcription	Fetal Muscle Trunk	muscle
4	chr10:25219200-25240000	Weak transcription	Dnd41	blood
5	chr10:25225400-25240000	Weak transcription	Duodenum Mucosa	Duodenum
6	chr10:25225400-25240000	Weak transcription	Fetal Brain Female	brain
7	chr10:25226200-25239800	Weak transcription	Fetal Lung	lung
8	chr10:25228200-25239800	Weak transcription	Fetal Stomach	stomach
9	chr10:25232600-25239800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr10:25232800-25240000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr10:25234200-25240400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr10:25234200-25240400	Weak transcription	Colon Smooth Muscle	Colon
13	chr10:25234200-25240600	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr10:25234200-25240600	Weak transcription	Right Atrium	heart
15	chr10:25234400-25239800	Weak transcription	A549	lung
16	chr10:25234400-25239800	Weak transcription	HepG2	liver
17	chr10:25234400-25239800	Weak transcription	K562	blood
18	chr10:25234400-25240600	Weak transcription	Adipose Nuclei	Adipose
19	chr10:25234600-25239800	Weak transcription	Fetal Intestine Small	intestine
20	chr10:25235400-25240400	Enhancers	Brain Substantia Nigra	brain
21	chr10:25236200-25241000	Weak transcription	Thymus	Thymus
22	chr10:25236600-25240200	Weak transcription	NHLF	lung
23	chr10:25236800-25239400	Enhancers	Brain Hippocampus Middle	brain
24	chr10:25236800-25239800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr10:25236800-25240000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr10:25236800-25240600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr10:25236800-25240600	Weak transcription	Left Ventricle	heart
28	chr10:25237000-25239800	Weak transcription	Fetal Muscle Leg	muscle
29	chr10:25237000-25240000	Weak transcription	Small Intestine	intestine
30	chr10:25237000-25240200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr10:25237000-25240400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr10:25237000-25240400	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr10:25237000-25240400	Weak transcription	Pancreas	Pancrea
34	chr10:25237000-25240400	Weak transcription	Osteobl	bone
35	chr10:25237000-25240600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr10:25237000-25240600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr10:25237000-25240600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr10:25237000-25240600	Weak transcription	NH-A	brain
39	chr10:25237000-25240800	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr10:25237000-25241000	Weak transcription	Ovary	ovary
41	chr10:25237200-25240000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr10:25237200-25240000	Weak transcription	NHDF-Ad	bronchial
43	chr10:25237200-25240400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr10:25237200-25240400	Weak transcription	GM12878-XiMat	blood
45	chr10:25237200-25240600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr10:25237200-25240600	Weak transcription	HUVEC	blood vessel
47	chr10:25237200-25240800	Weak transcription	HMEC	breast
48	chr10:25237400-25240600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr10:25237400-25240800	Weak transcription	NHEK	skin
50	chr10:25237400-25241400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links