Variant report

Variant	rs7178567
Chromosome Location	chr15:43236612-43236613
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:43234809..43237372-chr15:43248299..43250757,2	K562	blood:
2	chr15:43234709..43237589-chr15:43247590..43250522,2	MCF-7	breast:

Extended variants
information (count: 89 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1037990	0.91[EUR][1000 genomes]
rs10467975	0.93[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.87[LWK][hapmap];0.80[YRI][hapmap]
rs11070380	1.00[CEU][hapmap];0.88[CHB][hapmap];0.93[JPT][hapmap]
rs11070382	0.93[ASW][hapmap];1.00[CEU][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11070386	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs11070387	0.89[EUR][1000 genomes]
rs11070388	0.85[EUR][1000 genomes]
rs11070391	1.00[CEU][hapmap]
rs11630595	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11853250	0.86[ASW][hapmap];0.88[CEU][hapmap];0.86[JPT][hapmap];0.87[LWK][hapmap]
rs11854550	0.82[CHB][hapmap]
rs12050596	0.85[AFR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12594600	0.93[ASW][hapmap]
rs12905967	0.82[EUR][1000 genomes]
rs12913617	0.89[EUR][1000 genomes]
rs1381856	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1462856	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16957165	1.00[CEU][hapmap];0.88[CHB][hapmap];0.93[JPT][hapmap]
rs16957167	1.00[CEU][hapmap]
rs16957244	0.92[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.90[TSI][hapmap];0.85[YRI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16957250	1.00[CEU][hapmap];0.86[GIH][hapmap];0.94[MEX][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16957264	0.88[CEU][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];0.82[AMR][1000 genomes]
rs16957385	0.84[EUR][1000 genomes]
rs1972447	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1993813	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1996675	0.85[EUR][1000 genomes]
rs2035170	0.89[EUR][1000 genomes]
rs2037392	0.80[CEU][hapmap]
rs2054389	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2126602	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2412746	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2412747	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2412752	0.83[MEX][hapmap];0.81[TSI][hapmap]
rs2682073	0.86[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.81[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2733224	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28585036	1.00[CEU][hapmap];0.86[GIH][hapmap]
rs2899069	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3736054	1.00[ASW][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs3784265	0.89[EUR][1000 genomes]
rs3803341	1.00[CEU][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4244590	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4338775	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4509988	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4573908	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs4923955	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4924701	0.95[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs4924704	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55805543	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs60763334	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6416436	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6493065	0.86[ASW][hapmap]
rs6493071	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6493074	0.88[AMR][1000 genomes]
rs6493076	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];0.86[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6493077	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs66530524	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7162939	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7162959	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7174028	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.90[TSI][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7174915	1.00[CEU][hapmap]
rs7176116	0.83[EUR][1000 genomes]
rs7181238	0.86[ASW][hapmap];0.82[CHB][hapmap]
rs8027371	0.80[CEU][hapmap];1.00[CHB][hapmap]
rs8027733	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs8031767	0.93[ASW][hapmap];1.00[CEU][hapmap];0.86[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8035894	0.81[EUR][1000 genomes]
rs8036710	0.85[EUR][1000 genomes]
rs8037022	1.00[CEU][hapmap];0.87[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8042481	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9796571	0.82[EUR][1000 genomes]
rs9920092	0.82[CHB][hapmap]
rs9920498	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9920562	0.80[ASW][hapmap];0.82[CHB][hapmap]
rs9920624	0.82[CHB][hapmap]
rs9920904	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9920935	0.80[ASW][hapmap];0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050128	chr15:43056145-43262736	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv542368	chr15:43056145-43262736	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv525461	chr15:43062548-43482127	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
4	nsv904134	chr15:43097652-43357406	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv1044522	chr15:43115348-43658417	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	nsv515876	chr15:43116906-43445305	Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv904135	chr15:43143998-43392075	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv1036512	chr15:43164906-43274531	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv569239	chr15:43201109-43392075	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv569240	chr15:43201109-43445305	Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
11	nsv569241	chr15:43201109-43522922	Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
12	nsv1039587	chr15:43204351-43378274	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv569242	chr15:43210030-43445305	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7178567	GMFG	trans	lymphoblastoid	seeQTL
rs7178567	CCNDBP1	Cis_1M	lymphoblastoid	RTeQTL
rs7178567	TGM5	cis	lymphoblastoid	seeQTL
rs7178567	CCNDBP1	cis	multi-tissue	Pritchard
rs7178567	ELL3	cis	lymphoblastoid	seeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43223600-43238400	Weak transcription	Ovary	ovary
2	chr15:43225800-43247600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr15:43226000-43242200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr15:43227800-43236800	Weak transcription	Fetal Kidney	kidney
5	chr15:43228200-43237200	Weak transcription	NHEK	skin
6	chr15:43228200-43242400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr15:43229200-43237400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr15:43229800-43237400	Weak transcription	Brain Germinal Matrix	brain
9	chr15:43230000-43237400	Weak transcription	HSMMtube	muscle
10	chr15:43230200-43237200	Weak transcription	Stomach Smooth Muscle	stomach
11	chr15:43230200-43237400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr15:43230200-43237400	Weak transcription	Thymus	Thymus
13	chr15:43230200-43242400	Weak transcription	NHLF	lung
14	chr15:43230400-43237600	Weak transcription	Lung	lung
15	chr15:43230600-43236800	Weak transcription	Fetal Muscle Trunk	muscle
16	chr15:43230600-43237400	Weak transcription	Aorta	Aorta
17	chr15:43230600-43238400	Weak transcription	Fetal Intestine Small	intestine
18	chr15:43230800-43237400	Weak transcription	Small Intestine	intestine
19	chr15:43231800-43242600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr15:43232000-43238200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr15:43232000-43362800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr15:43232400-43237400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr15:43232400-43237400	Weak transcription	Fetal Stomach	stomach
24	chr15:43232400-43243400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr15:43232600-43242200	Weak transcription	Brain Anterior Caudate	brain
26	chr15:43233400-43236800	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr15:43233800-43237400	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr15:43234000-43237200	Weak transcription	Hela-S3	cervix
29	chr15:43234000-43242200	Weak transcription	Psoas Muscle	Psoas
30	chr15:43234000-43242400	Weak transcription	K562	blood
31	chr15:43234200-43241800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr15:43234200-43242400	Weak transcription	Brain Cingulate Gyrus	brain
33	chr15:43234200-43247600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr15:43234400-43239400	Strong transcription	Left Ventricle	heart
35	chr15:43234400-43242200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr15:43234400-43242200	Weak transcription	Rectal Smooth Muscle	rectum
37	chr15:43234600-43241800	Weak transcription	Brain Angular Gyrus	brain
38	chr15:43234600-43242400	Weak transcription	NHDF-Ad	bronchial
39	chr15:43234800-43238600	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr15:43234800-43239400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr15:43234800-43243400	Weak transcription	Gastric	stomach
42	chr15:43234800-43248400	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr15:43235000-43239200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr15:43235200-43237400	Weak transcription	Esophagus	oesophagus
45	chr15:43235200-43238600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr15:43235200-43239400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr15:43235200-43239600	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr15:43235400-43237800	Strong transcription	NH-A	brain
49	chr15:43235400-43238200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr15:43235400-43238400	Strong transcription	Fetal Thymus	thymus

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