Variant report

Variant	rs12715421
Chromosome Location	chr3:47084859-47084860
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 131 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs10433549	1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10461018	0.83[ASW][hapmap];0.89[CEU][hapmap];0.93[TSI][hapmap];0.91[YRI][hapmap]
rs1079276	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs1108301	0.82[EUR][1000 genomes]
rs11130110	0.89[CEU][hapmap];0.91[TSI][hapmap]
rs11130111	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs11130112	0.89[CEU][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs11130115	0.92[CEU][hapmap];0.93[TSI][hapmap]
rs11707736	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11709660	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11713693	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11714373	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11715121	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11719738	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11720139	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11917361	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11917474	0.82[EUR][1000 genomes]
rs11920354	0.83[AFR][1000 genomes]
rs11921117	0.81[AFR][1000 genomes]
rs11923706	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12152493	0.80[EUR][1000 genomes]
rs12493425	0.86[AFR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12631730	0.90[CHB][hapmap];0.95[CHD][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs13061071	0.92[CEU][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs13062681	0.86[EUR][1000 genomes]
rs13066214	0.83[EUR][1000 genomes]
rs13077398	0.82[EUR][1000 genomes]
rs13091054	0.88[EUR][1000 genomes]
rs13094438	0.81[CEU][hapmap];0.91[TSI][hapmap]
rs13098228	0.82[EUR][1000 genomes]
rs1466740	0.88[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs1466741	0.96[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs17784127	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1811652	0.86[AFR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1869869	0.82[EUR][1000 genomes]
rs2061197	0.91[ASW][hapmap];0.89[CEU][hapmap];0.93[TSI][hapmap];0.91[YRI][hapmap]
rs2088135	0.82[AFR][1000 genomes]
rs2132173	0.92[CEU][hapmap];0.91[TSI][hapmap]
rs2276853	0.81[CEU][hapmap];0.85[GIH][hapmap];0.91[TSI][hapmap]
rs2276854	0.81[CEU][hapmap];0.91[TSI][hapmap]
rs2278963	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2305634	0.92[CEU][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs2305635	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2305638	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs2385867	0.85[EUR][1000 genomes]
rs34103310	0.90[EUR][1000 genomes]
rs34344887	0.83[EUR][1000 genomes]
rs4018905	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4078466	0.89[CEU][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs4082155	0.89[CEU][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs4234465	0.89[CEU][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs4682831	0.82[EUR][1000 genomes]
rs4682837	0.89[CEU][hapmap]
rs4682844	0.91[ASW][hapmap];0.89[CEU][hapmap];0.91[TSI][hapmap];0.91[YRI][hapmap]
rs4682852	0.92[CEU][hapmap]
rs4683296	0.91[YRI][hapmap]
rs4683297	0.83[ASW][hapmap];0.91[YRI][hapmap]
rs4683322	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55724164	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55843455	0.82[EUR][1000 genomes]
rs55927279	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56217494	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56249396	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56250009	0.82[AFR][1000 genomes]
rs57756484	0.90[AFR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58956475	0.88[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61729713	0.82[EUR][1000 genomes]
rs62246375	0.82[EUR][1000 genomes]
rs62246398	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62246402	0.85[AFR][1000 genomes]
rs62246451	0.86[AFR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62246455	0.90[AFR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62248905	0.86[AFR][1000 genomes]
rs6414435	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6414436	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6442055	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6442059	0.86[AFR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6442060	0.84[ASN][1000 genomes]
rs66539935	0.82[EUR][1000 genomes]
rs66564457	0.81[EUR][1000 genomes]
rs6763236	0.90[EUR][1000 genomes]
rs6766230	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6767218	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6767907	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6768722	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6772670	0.95[CEU][hapmap]
rs6773521	0.90[AFR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6777145	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6781941	0.90[AFR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6785790	0.80[EUR][1000 genomes]
rs6791062	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6791842	0.81[CEU][hapmap]
rs6794193	0.89[EUR][1000 genomes]
rs73069104	0.82[AFR][1000 genomes]
rs7373821	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7426969	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7433300	1.00[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.86[MEX][hapmap];0.94[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs749511	0.84[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs749512	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.84[LWK][hapmap];0.86[MEX][hapmap];0.93[MKK][hapmap];0.85[TSI][hapmap];0.91[YRI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7610620	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7610636	0.86[EUR][1000 genomes]
rs7620997	0.91[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7621911	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7623888	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7625067	0.90[EUR][1000 genomes]
rs7625070	0.90[EUR][1000 genomes]
rs7628747	0.89[CEU][hapmap];0.91[TSI][hapmap]
rs7632501	0.86[AFR][1000 genomes]
rs7633435	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7633698	0.82[EUR][1000 genomes]
rs7636252	0.82[EUR][1000 genomes]
rs7637302	0.85[EUR][1000 genomes]
rs7645278	0.83[ASW][hapmap];0.91[YRI][hapmap]
rs9311403	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9812878	0.85[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9818382	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9821119	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9837343	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9843075	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9844122	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9845728	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9852082	0.86[YRI][hapmap]
rs9854790	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9858443	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9875235	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	esv3461834	chr3:46977730-47173228	Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3461835	chr3:46977822-47173168	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	esv3461836	chr3:46977822-47173168	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
5	nsv997261	chr3:47054766-47133680	Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv1007714	chr3:47084387-47331570	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12715421	SCAP	cis	parietal	SCAN
rs12715421	PRKAR2A	cis	cerebellum	SCAN
rs12715421	QRICH1	cis	parietal	SCAN
rs12715421	SETD2	Cis_1M	lymphoblastoid	RTeQTL
rs12715421	KLHL18	Cis_1M	lymphoblastoid	RTeQTL
rs12715421	C3orf75	cis	cerebellum	SCAN
rs12715421	HYAL2	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47069600-47088200	Strong transcription	Liver	Liver
2	chr3:47069600-47088200	Strong transcription	Fetal Intestine Large	intestine
3	chr3:47069600-47089000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:47069800-47086600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr3:47070400-47089000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr3:47073400-47087600	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr3:47073600-47087800	Strong transcription	Fetal Muscle Leg	muscle
8	chr3:47073600-47088200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr3:47073800-47088200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr3:47074200-47086600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr3:47074200-47086800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr3:47074400-47088600	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr3:47074600-47085400	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr3:47074600-47086600	Strong transcription	Duodenum Smooth Muscle	Duodenum
15	chr3:47074600-47088200	Strong transcription	NH-A	brain
16	chr3:47074600-47088400	Strong transcription	Placenta	Placenta
17	chr3:47074800-47088800	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr3:47075400-47088200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr3:47075600-47088200	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr3:47075800-47085000	Strong transcription	Cortex derived primary cultured neurospheres	brain
21	chr3:47075800-47086600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr3:47076000-47085000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr3:47078000-47130600	Weak transcription	Stomach Mucosa	stomach
24	chr3:47078400-47085800	Strong transcription	Fetal Stomach	stomach
25	chr3:47078800-47101400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr3:47079400-47088400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr3:47079400-47088800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr3:47079400-47095800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr3:47079600-47085400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr3:47079600-47088400	Weak transcription	Fetal Heart	heart
31	chr3:47079600-47088600	Weak transcription	Brain Substantia Nigra	brain
32	chr3:47079600-47088800	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr3:47079600-47123800	Weak transcription	Pancreas	Pancrea
34	chr3:47079600-47124200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:47079800-47095000	Weak transcription	HMEC	breast
36	chr3:47079800-47098000	Weak transcription	Aorta	Aorta
37	chr3:47079800-47124200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr3:47080000-47095200	Weak transcription	Fetal Brain Male	brain
39	chr3:47080400-47087000	Strong transcription	Primary B cells from peripheral blood	blood
40	chr3:47080800-47086800	Strong transcription	Primary T cells from cord blood	blood
41	chr3:47080800-47088600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr3:47081000-47085000	Strong transcription	HepG2	liver
43	chr3:47081000-47086800	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr3:47081000-47088800	Strong transcription	Primary T cells fromperipheralblood	blood
45	chr3:47081400-47085200	Strong transcription	Adipose Nuclei	Adipose
46	chr3:47081400-47085200	Strong transcription	Osteobl	bone
47	chr3:47081400-47086400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr3:47081400-47086600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr3:47081400-47086800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr3:47081400-47086800	Strong transcription	Primary T helper cells PMA-I stimulated	--

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