Variant report

Variant	rs4775876
Chromosome Location	chr15:50611716-50611717
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:50610712..50612973-chr15:50619651..50621682,2	MCF-7	breast:
2	chr15:50610363..50615933-chr15:50616213..50621203,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000104064	Chromatin interaction

Extended variants
information (count: 122 )
Associated
traits (count: 23 )

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs10152534	0.85[EUR][1000 genomes]
rs10220734	0.89[EUR][1000 genomes]
rs11070766	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11629603	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11630045	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11630063	0.83[ASN][1000 genomes]
rs11631197	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[ASN][1000 genomes]
rs11631985	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11632019	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11632703	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11633903	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs11636564	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11636908	1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11637901	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11637975	0.96[ASN][1000 genomes]
rs11638319	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs11638432	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11638564	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11639406	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11852487	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11853236	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11855823	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12594956	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs12902318	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12906304	1.00[JPT][hapmap];0.95[YRI][hapmap];0.87[ASN][1000 genomes]
rs12908591	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.91[ASN][1000 genomes]
rs12909337	0.91[ASN][1000 genomes]
rs12910368	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12910586	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12912679	0.91[ASN][1000 genomes]
rs12912855	0.89[AFR][1000 genomes]
rs12912969	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12913144	0.84[EUR][1000 genomes]
rs12923	1.00[JPT][hapmap];0.90[YRI][hapmap];0.87[ASN][1000 genomes]
rs1645	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16963604	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16963612	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17508371	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17509944	1.00[JPT][hapmap]
rs1797311	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs1972699	0.85[EUR][1000 genomes]
rs1972700	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2033115	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2081628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28372114	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28408662	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28451583	0.87[ASN][1000 genomes]
rs28453939	0.91[ASN][1000 genomes]
rs28531946	0.83[ASN][1000 genomes]
rs28534445	0.91[ASN][1000 genomes]
rs28609286	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28669213	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28688566	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28690939	0.91[ASN][1000 genomes]
rs28715646	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28716586	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28719982	0.91[ASN][1000 genomes]
rs28886692	0.91[EUR][1000 genomes]
rs34143694	0.91[ASN][1000 genomes]
rs34197276	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34312018	0.96[ASN][1000 genomes]
rs34405772	0.87[ASN][1000 genomes]
rs34590486	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35000991	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35024305	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35033384	0.87[ASN][1000 genomes]
rs35168369	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35354250	0.91[ASN][1000 genomes]
rs35446819	0.91[ASN][1000 genomes]
rs35453213	0.91[ASN][1000 genomes]
rs35777196	0.91[EUR][1000 genomes]
rs3784296	0.89[AFR][1000 genomes]
rs3784297	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs4774559	0.91[ASN][1000 genomes]
rs4775872	1.00[JPT][hapmap];0.90[YRI][hapmap];0.87[ASN][1000 genomes]
rs4775873	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.96[ASN][1000 genomes]
rs4775874	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4775875	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4775877	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs526045	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs526952	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[ASN][1000 genomes]
rs535648	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs62022571	0.84[ASN][1000 genomes]
rs62022573	0.86[EUR][1000 genomes]
rs6493425	0.90[EUR][1000 genomes]
rs6493427	0.83[EUR][1000 genomes]
rs6493429	1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6493430	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs7163457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7164375	0.83[ASN][1000 genomes]
rs7164377	0.83[ASN][1000 genomes]
rs7164798	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[ASN][1000 genomes]
rs7168233	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs7173127	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7175150	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7176792	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7179756	0.81[AMR][1000 genomes]
rs7183422	0.96[ASN][1000 genomes]
rs73399285	0.96[ASN][1000 genomes]
rs8024514	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[ASN][1000 genomes]
rs8025367	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8026571	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8026785	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs8027367	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8030036	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs8030952	0.87[ASN][1000 genomes]
rs8031431	0.88[EUR][1000 genomes]
rs8034597	0.87[ASN][1000 genomes]
rs8034615	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8036354	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8039829	0.90[EUR][1000 genomes]
rs8041259	0.81[EUR][1000 genomes]
rs8042053	0.96[ASN][1000 genomes]
rs8042451	0.85[EUR][1000 genomes]
rs8042845	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs8043257	0.85[EUR][1000 genomes]
rs8043475	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044277	chr15:49921547-50702386	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542380	chr15:49921547-50702386	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv1045456	chr15:50592472-51019873	Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
4	esv275353	chr15:50611393-50615498	Enhancers Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:23)

SNP	Gene	Cis/trans	Tissue	Source
rs4775876	GABPB1-AS1	cis	lung	GTEx
rs4775876	GABPB1-AS1	cis	Esophagus Mucosa	GTEx
rs4775876	CTD-3110H11.1	cis	Skin Sun Exposed Lower leg	GTEx
rs4775876	GABPB1-AS1	cis	Nerve Tibial	GTEx
rs4775876	CTD-3110H11.1	cis	Muscle Skeletal	GTEx
rs4775876	GABPB1-AS1	cis	Artery Tibial	GTEx
rs4775876	CTD-3110H11.1	cis	Nerve Tibial	GTEx
rs4775876	GABPB1-AS1	cis	Muscle Skeletal	GTEx
rs4775876	CTD-3110H11.1	cis	Esophagus Muscularis	GTEx
rs4775876	GABPB1-AS1	cis	Esophagus Muscularis	GTEx
rs4775876	GABPB1-AS1	cis	Whole Blood	GTEx
rs4775876	GABPB1-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs4775876	GABPB1-AS1	cis	Stomach	GTEx
rs4775876	CTD-3110H11.1	cis	lung	GTEx
rs4775876	GABPB1-AS1	cis	Artery Aorta	GTEx
rs4775876	CTD-3110H11.1	cis	Thyroid	GTEx
rs4775876	CTD-3110H11.1	cis	Artery Tibial	GTEx
rs4775876	CTD-3110H11.1	cis	Adipose Subcutaneous	GTEx
rs4775876	GABPB1-AS1	cis	Adipose Subcutaneous	GTEx
rs4775876	GABPB2	cis	lesional skin	skin_eQTL
rs4775876	GABPB2	cis	normal skin	skin_eQTL
rs4775876	CTD-3110H11.1	cis	Esophagus Mucosa	GTEx
rs4775876	GABPB2	cis	uninvolved skin	skin_eQTL

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50580800-50638400	Weak transcription	NHEK	skin
2	chr15:50596400-50623400	Weak transcription	Aorta	Aorta
3	chr15:50597000-50628600	Weak transcription	Fetal Stomach	stomach
4	chr15:50600800-50612800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr15:50600800-50613600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr15:50600800-50617200	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr15:50600800-50618600	Weak transcription	Fetal Intestine Large	intestine
8	chr15:50600800-50623200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr15:50600800-50629400	Weak transcription	Placenta	Placenta
10	chr15:50600800-50631200	Weak transcription	Left Ventricle	heart
11	chr15:50600800-50635400	Weak transcription	HepG2	liver
12	chr15:50600800-50641400	Weak transcription	HSMM	muscle
13	chr15:50600800-50641600	Weak transcription	Fetal Kidney	kidney
14	chr15:50600800-50643000	Weak transcription	Fetal Thymus	thymus
15	chr15:50600800-50643400	Weak transcription	Fetal Muscle Leg	muscle
16	chr15:50600800-50644200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr15:50600800-50644600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr15:50601000-50614400	Weak transcription	Psoas Muscle	Psoas
19	chr15:50601000-50622800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr15:50601000-50627200	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr15:50601000-50630400	Weak transcription	Primary B cells from peripheral blood	blood
22	chr15:50601000-50637000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr15:50601000-50638400	Weak transcription	HUVEC	blood vessel
24	chr15:50601400-50642800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr15:50602200-50621000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr15:50602200-50625600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr15:50608600-50623200	Weak transcription	A549	lung
28	chr15:50608800-50615600	Weak transcription	Duodenum Mucosa	Duodenum
29	chr15:50608800-50642800	Weak transcription	Hela-S3	cervix
30	chr15:50610400-50611800	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr15:50610800-50611800	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr15:50611000-50612600	Weak transcription	Primary B cells from cord blood	blood
33	chr15:50611200-50616200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr15:50611200-50640400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr15:50611200-50641200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr15:50611400-50626800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr15:50611400-50641200	Weak transcription	Primary T cells from cord blood	blood
38	chr15:50611600-50612800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr15:50611600-50613000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr15:50611600-50613400	Weak transcription	Primary hematopoietic stem cells	blood
41	chr15:50611600-50626800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr15:50611600-50630600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr15:50611600-50640000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links