Variant report

Variant	rs8034097
Chromosome Location	chr15:52437278-52437279
allele	A/G
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	TCF12	chr15:52435851-52437334	SK-N-SH	brain:	n/a	n/a
2	RCOR1	chr15:52435771-52437402	IMR90	lung:	n/a	n/a
3	TCF12	chr15:52435738-52437411	SK-N-SH	brain:	n/a	n/a
4	TFAP2A	chr15:52436866-52437372	Hela-S3	cervix:	n/a	chr15:52437115-52437130
5	FOSL2	chr15:52435930-52437356	SK-N-SH	brain:	n/a	n/a
6	TFAP2C	chr15:52436850-52437381	Hela-S3	cervix:	n/a	n/a
7	GATA3	chr15:52435830-52437376	SK-N-SH	brain:	n/a	chr15:52435922-52435943 chr15:52435927-52435936
8	FOS	chr15:52436899-52437292	Hela-S3	cervix:	n/a	n/a
9	JUND	chr15:52435749-52437338	SK-N-SH	brain:	n/a	chr15:52436307-52436318
10	NFIC	chr15:52436741-52437353	SK-N-SH	brain:	n/a	n/a
11	USF2	chr15:52436851-52437327	Hela-S3	cervix:	n/a	n/a
12	FOSL2	chr15:52436808-52437340	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:52433182..52434903-chr15:52435277..52437876,2	MCF-7	breast:

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

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs11070882	0.92[ASN][1000 genomes]
rs11856177	0.92[ASN][1000 genomes]
rs12438169	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12438190	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12438194	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12438743	0.91[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12438937	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12440354	0.80[ASN][1000 genomes]
rs12440956	0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12441074	0.80[ASN][1000 genomes]
rs12593041	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12594679	0.91[ASN][1000 genomes]
rs12595160	0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[ASN][1000 genomes]
rs12899030	1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[EUR][1000 genomes]
rs12899343	1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[EUR][1000 genomes]
rs12901354	0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12901730	0.90[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12901891	0.90[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12902073	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12902522	1.00[CEU][hapmap];0.80[ASN][1000 genomes]
rs12903769	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12904831	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12904889	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12905698	0.80[EUR][1000 genomes]
rs12907835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12908742	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12908833	0.92[ASN][1000 genomes]
rs12909161	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12909184	0.91[CEU][hapmap];1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs12909880	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12910398	1.00[CEU][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12912428	0.92[ASN][1000 genomes]
rs12916557	0.92[ASN][1000 genomes]
rs2227308	1.00[YRI][hapmap]
rs2398	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs34283892	0.91[ASN][1000 genomes]
rs35709612	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35827106	0.92[ASN][1000 genomes]
rs3794540	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3794543	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4636859	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4638520	1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[EUR][1000 genomes]
rs4774608	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4776003	0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4776007	0.91[CEU][hapmap];0.80[ASN][1000 genomes]
rs62014721	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62014722	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7164508	1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs7177248	0.83[CHB][hapmap]

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
rs8034097	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	chr15:52429600-52438400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr15:52429600-52440600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr15:52429800-52470200	Weak transcription	Fetal Brain Male	brain
17	chr15:52430000-52440800	Weak transcription	Brain Anterior Caudate	brain
18	chr15:52430000-52441400	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr15:52430000-52442800	Weak transcription	Fetal Heart	heart
20	chr15:52430000-52445800	Weak transcription	Small Intestine	intestine
21	chr15:52430200-52438600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr15:52430200-52440600	Weak transcription	Fetal Intestine Small	intestine
23	chr15:52430200-52441000	Weak transcription	Gastric	stomach
24	chr15:52430200-52441800	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr15:52430200-52442800	Strong transcription	Primary B cells from peripheral blood	blood
26	chr15:52430200-52442800	Weak transcription	Right Ventricle	heart
27	chr15:52430200-52444800	Weak transcription	Left Ventricle	heart
28	chr15:52430200-52446600	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr15:52430200-52457800	Weak transcription	Fetal Intestine Large	intestine
30	chr15:52430400-52441200	Weak transcription	Duodenum Mucosa	Duodenum
31	chr15:52431000-52446200	Strong transcription	Primary B cells from cord blood	blood
32	chr15:52431400-52446600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr15:52432200-52438600	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr15:52432200-52443000	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr15:52432200-52445400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr15:52432200-52453800	Weak transcription	Fetal Muscle Trunk	muscle
37	chr15:52432200-52455200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr15:52432200-52455200	Weak transcription	Colonic Mucosa	Colon
39	chr15:52432400-52439400	Weak transcription	Colon Smooth Muscle	Colon
40	chr15:52432400-52440400	Weak transcription	Adipose Nuclei	Adipose
41	chr15:52432600-52441000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr15:52432600-52441600	Weak transcription	Brain Angular Gyrus	brain
43	chr15:52433200-52437800	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr15:52434800-52437400	Strong transcription	Stomach Smooth Muscle	stomach
45	chr15:52434800-52446400	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr15:52435000-52446600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr15:52435400-52437400	Enhancers	HSMMtube	muscle
48	chr15:52435400-52437600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr15:52435400-52438000	Enhancers	Hela-S3	cervix
50	chr15:52435400-52439600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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