Variant report

Variant	rs13015822
Chromosome Location	chr2:113309653-113309654
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:113307316..113310204-chr2:113340273..113342615,2	MCF-7	breast:
2	chr2:113298945..113301583-chr2:113309336..113312263,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000125611	Chromatin interaction
ENSG00000125630	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12987214	0.93[AFR][1000 genomes]
rs12987434	0.93[AFR][1000 genomes]
rs13018087	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34117931	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34137042	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35684403	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs66571556	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

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	nsv949573	chr2:112986955-113320975	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv874877	chr2:113287964-113382054	Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13015822	RGPD4///RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL
rs13015822	RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113301200-113340200	Weak transcription	Right Atrium	heart
2	chr2:113301200-113341000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:113301400-113310000	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr2:113301400-113326200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr2:113301600-113316800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr2:113301600-113316800	Weak transcription	Stomach Mucosa	stomach
7	chr2:113301600-113325400	Weak transcription	Fetal Brain Male	brain
8	chr2:113301600-113325400	Weak transcription	Fetal Heart	heart
9	chr2:113303000-113320200	Strong transcription	K562	blood
10	chr2:113303000-113325400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr2:113303000-113325600	Strong transcription	Primary T cells from cord blood	blood
12	chr2:113303000-113334400	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr2:113303000-113334400	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr2:113303000-113335200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr2:113303200-113313200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr2:113303200-113320200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr2:113303200-113334200	Strong transcription	Cortex derived primary cultured neurospheres	brain
18	chr2:113303200-113334600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr2:113303400-113320200	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr2:113303400-113320200	Strong transcription	Fetal Intestine Large	intestine
21	chr2:113303400-113326200	Strong transcription	Primary B cells from cord blood	blood
22	chr2:113303400-113334400	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr2:113303400-113334600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr2:113303600-113311600	Strong transcription	Duodenum Smooth Muscle	Duodenum
25	chr2:113303600-113313400	Strong transcription	Brain Hippocampus Middle	brain
26	chr2:113303600-113314200	Strong transcription	NHEK	skin
27	chr2:113303600-113317000	Strong transcription	HUVEC	blood vessel
28	chr2:113303600-113317400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr2:113303600-113319800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr2:113303600-113320200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr2:113303600-113320400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
32	chr2:113303600-113320400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr2:113303600-113324400	Strong transcription	Fetal Brain Female	brain
34	chr2:113303600-113325400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr2:113303600-113325400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr2:113303600-113325800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr2:113303600-113326400	Strong transcription	Primary T helper cells PMA-I stimulated	--
38	chr2:113303600-113326600	Strong transcription	Primary B cells from peripheral blood	blood
39	chr2:113303600-113334000	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr2:113303600-113334400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr2:113303600-113334400	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr2:113303600-113334400	Strong transcription	Fetal Muscle Trunk	muscle
43	chr2:113303600-113334600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr2:113303600-113334600	Strong transcription	HUES6 Cell Line	embryonic stem cell
45	chr2:113303600-113334800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr2:113303600-113334800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
47	chr2:113303600-113335000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr2:113303600-113335000	Strong transcription	Fetal Thymus	thymus
49	chr2:113303600-113335200	Strong transcription	Fetal Muscle Leg	muscle
50	chr2:113303800-113313200	Strong transcription	Fetal Intestine Small	intestine

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