Variant report

Variant	rs17476940
Chromosome Location	chr15:49624784-49624785
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 128 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:125)

rs_ID	r²[population]
rs10519211	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10519221	0.81[EUR][1000 genomes]
rs10519229	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs1055254	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1114003	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11630318	0.81[CEU][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs11632038	0.81[EUR][1000 genomes]
rs11632575	0.83[EUR][1000 genomes]
rs11633282	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs11634636	0.82[EUR][1000 genomes]
rs11635005	0.81[CEU][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs11635308	0.81[CEU][hapmap];0.84[GIH][hapmap];0.88[MEX][hapmap];0.80[TSI][hapmap];0.81[EUR][1000 genomes]
rs11635354	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs11638314	0.82[EUR][1000 genomes]
rs11638606	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs1546424	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1546425	1.00[CHB][hapmap]
rs1580996	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1580997	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16962101	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16962112	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16962139	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16962146	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs16962147	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16962166	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16962169	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16962171	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16962174	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16962175	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16962177	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs16962187	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs16962189	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16962196	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16962202	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16962205	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16962209	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16962211	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16962213	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16962235	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16962236	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16962237	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16962238	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16962244	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16962256	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16962257	1.00[CHB][hapmap];0.88[CHD][hapmap];0.91[ASN][1000 genomes]
rs16962259	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16962262	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16962273	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16962274	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16962276	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16962288	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs16962296	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16962307	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16962308	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16962314	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16962327	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16962331	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16962416	1.00[CHB][hapmap]
rs17396612	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17396747	0.82[EUR][1000 genomes]
rs17397211	0.82[EUR][1000 genomes]
rs17400706	0.81[GIH][hapmap];0.94[MEX][hapmap]
rs17473568	0.81[MEX][hapmap];0.83[TSI][hapmap]
rs17475228	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17476361	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs17477722	0.81[CEU][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs17478618	0.81[GIH][hapmap];0.94[MEX][hapmap]
rs1835227	0.91[ASN][1000 genomes]
rs1874614	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2059935	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2078024	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2127243	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2163097	0.91[ASN][1000 genomes]
rs2169931	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2279192	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2413958	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2899437	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs3088333	1.00[MEX][hapmap];0.83[TSI][hapmap]
rs35692325	0.82[EUR][1000 genomes]
rs3784630	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4362337	1.00[JPT][hapmap]
rs4396481	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4774539	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs57252806	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs57560518	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57749497	0.82[EUR][1000 genomes]
rs59112977	0.84[EUR][1000 genomes]
rs59356430	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60594237	0.82[EUR][1000 genomes]
rs61259878	0.81[EUR][1000 genomes]
rs7162633	0.85[EUR][1000 genomes]
rs7167474	0.82[EUR][1000 genomes]
rs7167852	0.86[EUR][1000 genomes]
rs7168633	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7173759	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7176949	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7178101	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7179094	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7179907	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7181656	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7183899	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs73392233	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73392262	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73394324	0.82[EUR][1000 genomes]
rs73394331	0.82[EUR][1000 genomes]
rs73394333	0.82[EUR][1000 genomes]
rs73394339	0.82[EUR][1000 genomes]
rs73394355	0.82[EUR][1000 genomes]
rs73394357	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73394359	0.81[EUR][1000 genomes]
rs73396206	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73396235	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73396238	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs73398223	0.85[EUR][1000 genomes]
rs73398243	0.84[EUR][1000 genomes]
rs73398272	0.82[EUR][1000 genomes]
rs73398276	0.82[EUR][1000 genomes]
rs8025550	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8027094	0.84[EUR][1000 genomes]
rs8028746	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs8029506	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8030457	0.84[EUR][1000 genomes]
rs8031680	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs8033311	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8040436	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039220	chr15:49492509-49644261	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1039368	chr15:49566094-49764066	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv833002	chr15:49621400-49781799	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs17476940	C15orf33	cis	cerebellum	SCAN
rs17476940	DUOXA2	cis	cerebellum	SCAN
rs17476940	TNFAIP8L3	cis	parietal	SCAN
rs17476940	MFAP1	cis	cerebellum	SCAN
rs17476940	TRPM7	cis	cerebellum	SCAN
rs17476940	SECISBP2L	cis	parietal	SCAN
rs17476940	SPANXN3	trans	brain	seeQTL
rs17476940	LCMT2	cis	parietal	SCAN

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49562200-49626000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr15:49582600-49628200	Weak transcription	Spleen	Spleen
3	chr15:49597200-49624800	Weak transcription	Fetal Kidney	kidney
4	chr15:49599200-49636800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr15:49608000-49631800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr15:49608600-49631800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr15:49612200-49631600	Weak transcription	Fetal Intestine Small	intestine
8	chr15:49612200-49639000	Weak transcription	NHEK	skin
9	chr15:49612600-49639400	Weak transcription	Right Ventricle	heart
10	chr15:49612800-49626600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr15:49612800-49638000	Weak transcription	Brain Angular Gyrus	brain
12	chr15:49613000-49627600	Weak transcription	HUVEC	blood vessel
13	chr15:49613000-49628200	Weak transcription	Ovary	ovary
14	chr15:49613000-49633200	Weak transcription	Gastric	stomach
15	chr15:49613200-49625000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr15:49613200-49625000	Weak transcription	Hela-S3	cervix
17	chr15:49613200-49633200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr15:49613600-49625400	Weak transcription	Colon Smooth Muscle	Colon
19	chr15:49613600-49633800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr15:49613600-49637200	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr15:49613600-49643000	Weak transcription	Pancreas	Pancrea
22	chr15:49613800-49625000	Weak transcription	Fetal Brain Female	brain
23	chr15:49613800-49632600	Weak transcription	Fetal Thymus	thymus
24	chr15:49613800-49639800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr15:49614200-49631600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr15:49614200-49631600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr15:49614200-49631800	Weak transcription	Aorta	Aorta
28	chr15:49614200-49632000	Weak transcription	Fetal Muscle Leg	muscle
29	chr15:49614200-49637200	Weak transcription	Primary B cells from peripheral blood	blood
30	chr15:49614200-49640200	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr15:49614200-49640200	Weak transcription	Small Intestine	intestine
32	chr15:49614400-49633400	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr15:49614400-49634000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr15:49614800-49628800	Weak transcription	Osteobl	bone
35	chr15:49614800-49631800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr15:49614800-49639000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr15:49615600-49628400	Weak transcription	Adipose Nuclei	Adipose
38	chr15:49615800-49626600	Weak transcription	Fetal Stomach	stomach
39	chr15:49615800-49633600	Weak transcription	Placenta	Placenta
40	chr15:49615800-49636600	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr15:49616000-49641400	Weak transcription	Fetal Lung	lung
42	chr15:49616600-49632000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr15:49617800-49633000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr15:49618000-49626800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr15:49622400-49631600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr15:49622600-49631600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr15:49622600-49631600	Weak transcription	Fetal Intestine Large	intestine
48	chr15:49622600-49631800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr15:49622600-49632200	Weak transcription	Thymus	Thymus
50	chr15:49622600-49642600	Weak transcription	HSMM	muscle

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