Variant report

Variant	rs8041325
Chromosome Location	chr15:41732386-41732387
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10467974	0.86[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs10518718	0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs11631770	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap]
rs11633799	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap]
rs13379756	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.98[TSI][hapmap]
rs16971767	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs16971798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap]
rs16971806	0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs16971832	0.91[JPT][hapmap]
rs16971834	0.86[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap]
rs1757456	0.84[CEU][hapmap];0.80[CHB][hapmap]
rs1757463	0.87[CHB][hapmap];0.85[LWK][hapmap]
rs2015781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2777491	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap]
rs28526381	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs28557159	0.88[ASW][hapmap];0.81[GIH][hapmap]
rs316605	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs316609	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs316610	0.94[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs316614	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs316617	0.81[CEU][hapmap];0.87[CHB][hapmap];0.86[TSI][hapmap]
rs35826725	0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs3743038	0.88[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap]
rs7163788	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs7167498	0.93[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs7168307	0.83[ASW][hapmap];0.80[GIH][hapmap]
rs7175800	0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs7176588	0.95[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs7177641	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs7178634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs7178777	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs7180418	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs8023530	0.83[ASW][hapmap];0.81[GIH][hapmap]
rs8024774	0.84[CEU][hapmap];0.80[CHB][hapmap];0.86[TSI][hapmap]
rs8026197	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs8032838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs8036498	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs8037574	0.83[ASW][hapmap];0.81[GIH][hapmap]
rs823716	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap]
rs919961	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap]
rs9302109	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][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	nsv1044438	chr15:41560160-41745480	Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
2	nsv1038923	chr15:41585028-41754890	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv1045142	chr15:41585044-41738314	Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
4	nsv1039283	chr15:41620499-41745480	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases
5	nsv933757	chr15:41641236-41773058	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	27 gene(s)	inside rSNPs	diseases
6	nsv524476	chr15:41689232-41820200	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs8041325	STARD9	cis	cerebellum	SCAN
rs8041325	NDUFAF1	cis	multi-tissue	Pritchard
rs8041325	RPAP1	cis	parietal	SCAN
rs8041325	KRTAP4-7	Cis_1M	lymphoblastoid	RTeQTL
rs8041325	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL
rs8041325	NDUFAF1	cis	Esophagus Muscularis	GTEx
rs8041325	OIP5-AS1	cis	Nerve Tibial	GTEx
rs8041325	NDUFAF1	cis	Thyroid	GTEx
rs8041325	OIP5-AS1	cis	Artery Tibial	GTEx
rs8041325	NUSAP1	cis	parietal	SCAN
rs8041325	NDUFAF1	cis	parietal	SCAN
rs8041325	LOC729082	Cis_1M	lymphoblastoid	RTeQTL
rs8041325	NUSAP1	cis	cerebellum	SCAN
rs8041325	NDUFAF1	cis	Heart Left Ventricle	GTEx
rs8041325	OIP5-AS1	cis	Adipose Subcutaneous	GTEx
rs8041325	NDUFAF1	cis	Muscle Skeletal	GTEx
rs8041325	NDUFAF1	cis	cerebellum	SCAN
rs8041325	NDUFAF1	cis	lymphoblastoid	seeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41710400-41745200	Weak transcription	Esophagus	oesophagus
2	chr15:41710400-41750000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:41710600-41733600	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr15:41710600-41745200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr15:41710800-41733400	Weak transcription	Brain Hippocampus Middle	brain
6	chr15:41710800-41733400	Weak transcription	HSMMtube	muscle
7	chr15:41711400-41733400	Weak transcription	Brain Angular Gyrus	brain
8	chr15:41711400-41733400	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr15:41711600-41746800	Weak transcription	A549	lung
10	chr15:41711600-41759000	Weak transcription	Fetal Heart	heart
11	chr15:41711800-41735400	Weak transcription	Fetal Kidney	kidney
12	chr15:41712800-41733600	Weak transcription	Fetal Lung	lung
13	chr15:41713200-41745200	Weak transcription	Spleen	Spleen
14	chr15:41716600-41733600	Weak transcription	HepG2	liver
15	chr15:41716800-41733400	Weak transcription	Hela-S3	cervix
16	chr15:41718200-41745200	Weak transcription	Pancreas	Pancrea
17	chr15:41719000-41733400	Weak transcription	HMEC	breast
18	chr15:41719000-41733400	Weak transcription	HSMM	muscle
19	chr15:41719000-41733400	Weak transcription	NHEK	skin
20	chr15:41719000-41733800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr15:41719000-41745200	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr15:41719000-41749800	Weak transcription	NHLF	lung
23	chr15:41719000-41765800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr15:41719200-41734000	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr15:41721600-41735400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr15:41721600-41745200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr15:41721800-41735000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr15:41722000-41733400	Weak transcription	Fetal Brain Male	brain
29	chr15:41722000-41733600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr15:41722000-41733600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr15:41722000-41735200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr15:41722000-41749200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr15:41722000-41749600	Weak transcription	Gastric	stomach
34	chr15:41722000-41768400	Weak transcription	Small Intestine	intestine
35	chr15:41722200-41733600	Weak transcription	Right Ventricle	heart
36	chr15:41724200-41777200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr15:41727400-41735400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr15:41728200-41749800	Weak transcription	Rectal Smooth Muscle	rectum
39	chr15:41728400-41733600	Weak transcription	Colon Smooth Muscle	Colon
40	chr15:41729200-41773000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr15:41729400-41735600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr15:41729400-41756200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr15:41729600-41735200	Strong transcription	Brain Germinal Matrix	brain
44	chr15:41729600-41736000	Strong transcription	Dnd41	blood
45	chr15:41729800-41732400	Strong transcription	Stomach Smooth Muscle	stomach
46	chr15:41729800-41734400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr15:41729800-41735200	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr15:41729800-41735600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr15:41729800-41735600	Strong transcription	Fetal Brain Female	brain
50	chr15:41729800-41735800	Strong transcription	HUES6 Cell Line	embryonic stem cell

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