Variant report

Variant	rs1571015
Chromosome Location	chr10:90792175-90792176
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:90790531..90793137-chr10:90969474..90972044,2	MCF-7	breast:
2	chr10:90791836..90792785-chr10:90972789..90973327,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAS-2	chr10:90787438-90793194	NONHSAT015495

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11814536	0.90[ASN][1000 genomes]
rs11814780	0.83[JPT][hapmap]
rs12360387	0.90[ASN][1000 genomes]
rs17378454	0.83[JPT][hapmap]
rs17380969	0.91[JPT][hapmap]
rs17449853	0.85[EUR][1000 genomes]
rs17465703	0.83[JPT][hapmap]
rs1926189	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7085850	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042848	chr10:90466032-91318474	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv540741	chr10:90466032-91318474	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS 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	66 gene(s)	inside rSNPs	diseases
3	nsv831943	chr10:90664836-90865834	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1571015	RP11-80H5.9	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90771800-90808600	Weak transcription	Primary T cells from cord blood	blood
2	chr10:90772400-90795000	Weak transcription	Placenta	Placenta
3	chr10:90772600-90795800	Weak transcription	Rectal Smooth Muscle	rectum
4	chr10:90776600-90792600	Weak transcription	Right Ventricle	heart
5	chr10:90780600-90792400	Weak transcription	Duodenum Mucosa	Duodenum
6	chr10:90780800-90804200	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr10:90788400-90792800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr10:90788800-90792800	Enhancers	NHDF-Ad	bronchial
9	chr10:90789400-90792800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr10:90789400-90793000	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr10:90789400-90793000	Enhancers	Osteobl	bone
12	chr10:90789600-90792800	Enhancers	Primary B cells from cord blood	blood
13	chr10:90789800-90792200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr10:90789800-90792600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr10:90789800-90793000	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr10:90789800-90802000	Weak transcription	Ovary	ovary
17	chr10:90790000-90792600	Weak transcription	Brain Hippocampus Middle	brain
18	chr10:90790000-90802800	Weak transcription	Fetal Intestine Small	intestine
19	chr10:90790400-90792800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
20	chr10:90790600-90792600	Enhancers	Adipose Nuclei	Adipose
21	chr10:90790600-90792800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr10:90790600-90792800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr10:90790800-90792200	Enhancers	HUVEC	blood vessel
24	chr10:90790800-90792800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr10:90791200-90792200	Enhancers	A549	lung
26	chr10:90791200-90792800	Enhancers	HUES64 Cell Line	embryonic stem cell
27	chr10:90791200-90792800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr10:90791200-90793000	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr10:90791200-90793200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr10:90791400-90792200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr10:90791400-90792400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr10:90791400-90792600	Enhancers	HSMMtube	muscle
33	chr10:90791400-90792800	Enhancers	H1 Cell Line	embryonic stem cell
34	chr10:90791400-90792800	Enhancers	H9 Cell Line	embryonic stem cell
35	chr10:90791400-90792800	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr10:90791400-90792800	Enhancers	Stomach Mucosa	stomach
37	chr10:90791400-90792800	Enhancers	Spleen	Spleen
38	chr10:90791400-90792800	Enhancers	NHLF	lung
39	chr10:90791600-90792400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
40	chr10:90791600-90792400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
41	chr10:90791600-90792600	Enhancers	Primary T helper cells PMA-I stimulated	--
42	chr10:90791600-90792800	Enhancers	Primary hematopoietic stem cells	blood
43	chr10:90791600-90792800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
44	chr10:90791600-90792800	Enhancers	Fetal Lung	lung
45	chr10:90791600-90792800	Enhancers	Rectal Mucosa Donor 31	rectum
46	chr10:90791600-90793000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr10:90791600-90793000	Enhancers	Duodenum Smooth Muscle	Duodenum
48	chr10:90791800-90792200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
49	chr10:90791800-90792200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
50	chr10:90791800-90792200	Enhancers	Primary T regulatory cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links