Variant report

Variant	rs2163388
Chromosome Location	chr3:113549718-113549719
allele	C/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	chr3:113548993..113551007-chr3:113552942..113555704,2	K562	blood:

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11706726	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12631130	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2399490	0.82[ASN][1000 genomes]
rs2399491	0.82[ASN][1000 genomes]
rs2712334	0.81[ASN][1000 genomes]
rs2712366	0.83[ASN][1000 genomes]
rs4339084	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4682502	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62265385	0.82[ASN][1000 genomes]
rs736360	0.81[ASN][1000 genomes]
rs7628746	0.81[ASN][1000 genomes]
rs7632377	0.83[AFR][1000 genomes]
rs7636168	0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7646203	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2163388	GRAMD1C	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:113546800-113550000	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr3:113546800-113550000	Enhancers	Primary B cells from peripheral blood	blood
3	chr3:113546800-113550200	Flanking Active TSS	GM12878-XiMat	blood
4	chr3:113548200-113551200	Enhancers	HUVEC	blood vessel
5	chr3:113548600-113550000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr3:113548600-113550000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr3:113548600-113550000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr3:113548600-113550000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr3:113548600-113550200	Enhancers	NHEK	skin
10	chr3:113548600-113550400	Enhancers	HMEC	breast
11	chr3:113548600-113550600	Enhancers	Hela-S3	cervix
12	chr3:113548600-113550800	Enhancers	Muscle Satellite Cultured Cells	--
13	chr3:113548600-113552600	Enhancers	HepG2	liver
14	chr3:113548800-113549800	Enhancers	H9 Cell Line	embryonic stem cell
15	chr3:113548800-113549800	Enhancers	HSMM	muscle
16	chr3:113548800-113550000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr3:113548800-113550000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr3:113548800-113550000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr3:113548800-113550200	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr3:113548800-113550200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr3:113548800-113550600	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr3:113548800-113551000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:113549000-113550000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr3:113549000-113550000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr3:113549000-113550000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr3:113549000-113550000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
27	chr3:113549000-113550000	Enhancers	Osteobl	bone
28	chr3:113549000-113550200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
29	chr3:113549200-113549800	Enhancers	iPS-20b Cell Line	embryonic stem cell
30	chr3:113549200-113549800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr3:113549200-113549800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
32	chr3:113549200-113549800	Enhancers	NHDF-Ad	bronchial
33	chr3:113549200-113550200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr3:113549400-113550000	Enhancers	Stomach Mucosa	stomach
35	chr3:113549400-113550200	Enhancers	HUES6 Cell Line	embryonic stem cell
36	chr3:113549400-113550400	Enhancers	HUES64 Cell Line	embryonic stem cell
37	chr3:113549400-113551600	Weak transcription	Primary hematopoietic stem cells	blood
38	chr3:113549400-113557600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr3:113549600-113549800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr3:113549600-113550000	Enhancers	Primary T cells fromperipheralblood	blood
41	chr3:113549600-113550400	Enhancers	Primary B cells from cord blood	blood
42	chr3:113549600-113557000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links