Variant report

Variant	rs12631130
Chromosome Location	chr3:113551182-113551183
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	chr3:113538794..113541088-chr3:113549599..113551887,2	MCF-7	breast:
2	chr3:113546118..113548286-chr3:113550163..113552651,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000178075	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11706726	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2163388	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2399490	0.80[ASN][1000 genomes]
rs2399491	0.80[ASN][1000 genomes]
rs2712366	0.81[ASN][1000 genomes]
rs4339084	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4682502	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62265385	0.80[ASN][1000 genomes]
rs7632377	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7636168	0.81[AMR][1000 genomes]
rs7646203	0.81[EUR][1000 genomes]
rs9883363	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv482804	chr3:113432431-113581672	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv829678	chr3:113446177-113633053	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv877351	chr3:113450495-113637424	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv1013746	chr3:113460162-113646657	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	nsv432478	chr3:113492402-113614489	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
7	nsv460822	chr3:113543081-113600970	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv591302	chr3:113543081-113600970	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12631130	GRAMD1C	cis	Adipose Subcutaneous	GTEx
rs12631130	GRAMD1C	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:113548200-113551200	Enhancers	HUVEC	blood vessel
2	chr3:113548600-113552600	Enhancers	HepG2	liver
3	chr3:113549400-113551600	Weak transcription	Primary hematopoietic stem cells	blood
4	chr3:113549400-113557600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr3:113549600-113557000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr3:113549800-113557600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr3:113549800-113557600	Weak transcription	NHDF-Ad	bronchial
8	chr3:113550000-113551200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr3:113550000-113551600	Enhancers	Primary neutrophils fromperipheralblood	blood
10	chr3:113550000-113553000	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr3:113550000-113554200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr3:113550000-113554200	Weak transcription	Stomach Mucosa	stomach
13	chr3:113550000-113557200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr3:113550000-113557400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr3:113550000-113557600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr3:113550000-113557600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr3:113550200-113551200	Enhancers	GM12878-XiMat	blood
18	chr3:113550200-113551400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr3:113550200-113551600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr3:113550200-113551600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr3:113550200-113553800	Weak transcription	NHEK	skin
22	chr3:113550400-113551400	Weak transcription	HMEC	breast
23	chr3:113550600-113551600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr3:113550600-113553800	Weak transcription	Hela-S3	cervix
25	chr3:113550800-113552600	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr3:113551000-113551200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr3:113551000-113551200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr3:113551000-113551600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr3:113551000-113552200	Enhancers	Primary B cells from peripheral blood	blood
30	chr3:113551000-113552600	Enhancers	Primary T cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links