Variant report

Variant	rs12438190
Chromosome Location	chr15:52439065-52439066
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	PBX3	chr15:52439020-52439373	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:52377651..52380251-chr15:52438624..52441229,2	MCF-7	breast:
2	chr15:52429617..52433852-chr15:52437614..52441037,3	MCF-7	breast:
3	chr15:52438653..52441252-chr15:52442055..52444033,2	MCF-7	breast:

Variant related genes	Relation type
GNB5	TF binding region
ENSG00000069966	Chromatin interaction
ENSG00000259709	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs12438169	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12438194	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12438274	0.83[ASN][1000 genomes]
rs12438937	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12440354	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12441074	0.91[ASN][1000 genomes]
rs12593041	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12899030	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12899343	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12902522	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12904831	0.86[EUR][1000 genomes]
rs12904889	0.84[EUR][1000 genomes]
rs12905698	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12907835	0.86[EUR][1000 genomes]
rs12909161	0.86[EUR][1000 genomes]
rs12909184	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12910052	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12910398	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12910870	0.83[ASN][1000 genomes]
rs2414132	0.85[ASN][1000 genomes]
rs35709612	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35733550	0.83[ASN][1000 genomes]
rs3794540	0.86[EUR][1000 genomes]
rs3794543	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4238384	0.89[ASN][1000 genomes]
rs4506834	0.83[ASN][1000 genomes]
rs4636859	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4638520	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4774608	0.86[EUR][1000 genomes]
rs4776007	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4776008	0.83[ASN][1000 genomes]
rs62014721	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62014722	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7166799	0.83[ASN][1000 genomes]
rs7177248	0.84[ASN][1000 genomes]
rs8029782	0.84[ASN][1000 genomes]
rs8034097	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471244	chr15:52305463-52511465	Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv984198	chr15:52319726-52481137	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription 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	23 gene(s)	inside rSNPs	diseases
3	nsv1054372	chr15:52369078-52579464	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv542387	chr15:52369078-52579464	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv833005	chr15:52389869-52541330	Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv1047647	chr15:52425879-52469181	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12438190	GNB5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52407600-52441600	Weak transcription	Fetal Lung	lung
2	chr15:52407800-52440400	Weak transcription	Brain Substantia Nigra	brain
3	chr15:52410200-52441600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr15:52410600-52441400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr15:52412000-52441200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr15:52422600-52457600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr15:52423000-52458200	Weak transcription	Dnd41	blood
8	chr15:52424000-52441200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr15:52427400-52441600	Weak transcription	Esophagus	oesophagus
10	chr15:52428800-52440600	Weak transcription	Spleen	Spleen
11	chr15:52429000-52446400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr15:52429000-52447200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr15:52429200-52447400	Strong transcription	Primary T cells from cord blood	blood
14	chr15:52429600-52440600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr15:52429800-52470200	Weak transcription	Fetal Brain Male	brain
16	chr15:52430000-52440800	Weak transcription	Brain Anterior Caudate	brain
17	chr15:52430000-52441400	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr15:52430000-52442800	Weak transcription	Fetal Heart	heart
19	chr15:52430000-52445800	Weak transcription	Small Intestine	intestine
20	chr15:52430200-52440600	Weak transcription	Fetal Intestine Small	intestine
21	chr15:52430200-52441000	Weak transcription	Gastric	stomach
22	chr15:52430200-52441800	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr15:52430200-52442800	Strong transcription	Primary B cells from peripheral blood	blood
24	chr15:52430200-52442800	Weak transcription	Right Ventricle	heart
25	chr15:52430200-52444800	Weak transcription	Left Ventricle	heart
26	chr15:52430200-52446600	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr15:52430200-52457800	Weak transcription	Fetal Intestine Large	intestine
28	chr15:52430400-52441200	Weak transcription	Duodenum Mucosa	Duodenum
29	chr15:52431000-52446200	Strong transcription	Primary B cells from cord blood	blood
30	chr15:52431400-52446600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr15:52432200-52443000	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr15:52432200-52445400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr15:52432200-52453800	Weak transcription	Fetal Muscle Trunk	muscle
34	chr15:52432200-52455200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr15:52432200-52455200	Weak transcription	Colonic Mucosa	Colon
36	chr15:52432400-52439400	Weak transcription	Colon Smooth Muscle	Colon
37	chr15:52432400-52440400	Weak transcription	Adipose Nuclei	Adipose
38	chr15:52432600-52441000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr15:52432600-52441600	Weak transcription	Brain Angular Gyrus	brain
40	chr15:52434800-52446400	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr15:52435000-52446600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr15:52435400-52439600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr15:52435400-52444200	Strong transcription	Fetal Stomach	stomach
44	chr15:52435400-52445600	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr15:52435400-52446200	Strong transcription	Brain Germinal Matrix	brain
46	chr15:52435400-52446200	Strong transcription	Fetal Brain Female	brain
47	chr15:52435600-52445600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr15:52435800-52439400	Strong transcription	Fetal Thymus	thymus
49	chr15:52435800-52443800	Strong transcription	Brain Inferior Temporal Lobe	brain
50	chr15:52435800-52445800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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