Variant report

Variant	rs933807
Chromosome Location	chr15:62274940-62274941
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:62268988..62271189-chr15:62273485..62276457,2	MCF-7	breast:

Extended variants
information (count: 105 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10047986	0.85[EUR][1000 genomes]
rs1030859	0.85[EUR][1000 genomes]
rs10468026	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11071642	0.81[CEU][hapmap]
rs11071649	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11629596	0.84[EUR][1000 genomes]
rs11633500	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11635977	0.85[EUR][1000 genomes]
rs11638793	0.92[YRI][hapmap]
rs11639482	1.00[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12438690	0.83[EUR][1000 genomes]
rs12438803	0.85[EUR][1000 genomes]
rs12439356	0.93[CEU][hapmap];0.80[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs12442212	0.93[CEU][hapmap];0.80[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs12442675	0.96[CEU][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12592402	1.00[CEU][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12593844	0.81[CEU][hapmap];0.93[GIH][hapmap];0.83[MEX][hapmap]
rs12594658	0.96[CEU][hapmap];0.91[JPT][hapmap];0.92[YRI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12594946	0.85[AMR][1000 genomes]
rs12899801	0.81[CEU][hapmap];0.93[GIH][hapmap];0.83[MEX][hapmap]
rs12900645	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12908182	0.81[EUR][1000 genomes]
rs12910541	0.83[EUR][1000 genomes]
rs12912208	0.85[CEU][hapmap];0.93[GIH][hapmap];0.82[MEX][hapmap]
rs12913951	0.85[EUR][1000 genomes]
rs1344601	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1436958	0.98[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.81[TSI][hapmap];0.84[AMR][1000 genomes]
rs1436963	0.85[EUR][1000 genomes]
rs1436964	0.85[EUR][1000 genomes]
rs1436966	0.85[CEU][hapmap];0.95[GIH][hapmap];0.88[MEX][hapmap]
rs1534542	0.86[JPT][hapmap]
rs17205407	0.85[EUR][1000 genomes]
rs17205463	0.83[EUR][1000 genomes]
rs17271340	0.85[CEU][hapmap]
rs17271403	0.84[EUR][1000 genomes]
rs17271438	0.83[EUR][1000 genomes]
rs2162062	1.00[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2414753	0.82[CEU][hapmap]
rs2414754	0.85[CEU][hapmap]
rs28542204	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28837073	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2899677	0.84[AMR][1000 genomes]
rs34096515	0.84[EUR][1000 genomes]
rs34138933	0.84[AMR][1000 genomes]
rs35123892	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3784445	0.81[CEU][hapmap]
rs3784633	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3784634	0.81[CEU][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs4143842	0.84[EUR][1000 genomes]
rs4143843	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4564516	0.85[EUR][1000 genomes]
rs4774427	0.82[CEU][hapmap];0.86[TSI][hapmap]
rs4775455	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4775457	0.85[EUR][1000 genomes]
rs4775458	0.85[EUR][1000 genomes]
rs62007368	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7162536	0.85[EUR][1000 genomes]
rs7172967	0.81[CEU][hapmap];0.87[TSI][hapmap]
rs7177276	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7177711	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs7178424	0.93[CEU][hapmap];0.80[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7178540	0.93[CEU][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7178945	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs731820	0.93[CEU][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs8025877	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs8026008	0.92[CEU][hapmap];0.81[JPT][hapmap];0.85[EUR][1000 genomes]
rs8029942	0.85[CEU][hapmap];0.93[GIH][hapmap];0.83[MEX][hapmap]
rs8032433	1.00[ASW][hapmap];0.96[CEU][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8033816	0.91[GIH][hapmap]
rs8034216	0.85[CEU][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes]
rs8034335	0.85[CEU][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs8038932	0.85[EUR][1000 genomes]
rs8039105	0.85[CEU][hapmap]
rs8039651	0.96[CEU][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs893156	0.93[CEU][hapmap];0.82[JPT][hapmap];0.84[YRI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs893157	0.81[CEU][hapmap]
rs893158	0.93[CEU][hapmap];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:28 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521334	chr15:62129809-62340126	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv527451	chr15:62129809-62340126	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv904286	chr15:62146598-62313373	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv904287	chr15:62146598-62338797	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
5	nsv904288	chr15:62146598-62356386	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
6	nsv569641	chr15:62155282-62287456	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv904289	chr15:62156690-62287456	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
8	nsv516639	chr15:62175134-62340126	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv904290	chr15:62175134-62356386	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv904291	chr15:62178695-62287456	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv904292	chr15:62178695-62313373	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv904293	chr15:62178695-62338797	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv904294	chr15:62178695-62356386	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
14	nsv457176	chr15:62178695-62519658	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
15	nsv569643	chr15:62178695-62519658	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
16	nsv904296	chr15:62198564-62313373	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
17	nsv471247	chr15:62202481-62519658	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
18	nsv904297	chr15:62202482-62313373	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
19	nsv569645	chr15:62202482-62319307	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
20	nsv569646	chr15:62202482-62519658	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS 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	12 gene(s)	inside rSNPs	diseases
21	esv1816724	chr15:62205104-62285146	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
22	nsv569647	chr15:62214607-62284101	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
23	nsv904298	chr15:62218689-62338797	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
24	nsv569648	chr15:62239697-62340126	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
25	nsv457177	chr15:62243197-62301094	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
26	nsv569649	chr15:62243197-62301094	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
27	nsv569650	chr15:62243197-62313373	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
28	nsv569651	chr15:62243197-62313417	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs933807	TEX9	cis	parietal	SCAN
rs933807	USP3	cis	cerebellum	SCAN
rs933807	VPS13C	cis	cerebellum	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:62150000-62276200	Weak transcription	Psoas Muscle	Psoas
2	chr15:62185600-62333600	Weak transcription	Right Ventricle	heart
3	chr15:62185800-62300000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr15:62188600-62309400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr15:62195600-62285400	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr15:62208200-62290200	Weak transcription	Aorta	Aorta
7	chr15:62221400-62327600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr15:62229400-62280200	Weak transcription	K562	blood
9	chr15:62230800-62317200	Weak transcription	Pancreas	Pancrea
10	chr15:62235600-62277400	Strong transcription	Primary B cells from peripheral blood	blood
11	chr15:62235800-62285000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr15:62244600-62350400	Weak transcription	Small Intestine	intestine
13	chr15:62244800-62278600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr15:62245800-62278400	Strong transcription	Dnd41	blood
15	chr15:62248000-62281400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr15:62254000-62303600	Weak transcription	Spleen	Spleen
17	chr15:62254200-62287800	Weak transcription	Lung	lung
18	chr15:62254200-62297800	Weak transcription	Fetal Intestine Small	intestine
19	chr15:62255200-62275800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr15:62255800-62276600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr15:62257200-62276000	Weak transcription	HSMMtube	muscle
22	chr15:62259200-62276000	Weak transcription	HMEC	breast
23	chr15:62259400-62276000	Weak transcription	Brain Substantia Nigra	brain
24	chr15:62259400-62327200	Weak transcription	HepG2	liver
25	chr15:62259600-62276000	Weak transcription	Brain Angular Gyrus	brain
26	chr15:62259600-62278200	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr15:62261000-62279600	Weak transcription	Esophagus	oesophagus
28	chr15:62261400-62276600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr15:62262200-62276400	Strong transcription	Duodenum Mucosa	Duodenum
30	chr15:62262600-62312600	Weak transcription	NHEK	skin
31	chr15:62263800-62276000	Weak transcription	Thymus	Thymus
32	chr15:62263800-62287800	Weak transcription	Fetal Stomach	stomach
33	chr15:62263800-62290200	Weak transcription	Gastric	stomach
34	chr15:62264000-62276000	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr15:62264000-62281600	Weak transcription	Fetal Brain Female	brain
36	chr15:62264000-62287000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr15:62264000-62312600	Weak transcription	Rectal Smooth Muscle	rectum
38	chr15:62264000-62323800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr15:62264000-62324000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr15:62264400-62281800	Weak transcription	Fetal Brain Male	brain
41	chr15:62264800-62275400	Weak transcription	Ovary	ovary
42	chr15:62264800-62276000	Weak transcription	Colon Smooth Muscle	Colon
43	chr15:62264800-62282000	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr15:62264800-62286200	Weak transcription	Osteobl	bone
45	chr15:62264800-62299400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr15:62265000-62283600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr15:62265000-62299400	Weak transcription	Brain Germinal Matrix	brain
48	chr15:62265000-62299800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr15:62265200-62276000	Weak transcription	NHLF	lung
50	chr15:62265600-62299600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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