Variant report

Variant	rs4683322
Chromosome Location	chr3:47093189-47093190
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 133 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:127)

rs_ID	r²[population]
rs10433549	1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10461018	0.83[ASW][hapmap];0.89[CEU][hapmap];0.91[TSI][hapmap];0.91[YRI][hapmap]
rs1079276	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs1108301	0.81[EUR][1000 genomes]
rs11130110	0.89[CEU][hapmap];0.89[TSI][hapmap]
rs11130111	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs11130112	0.89[CEU][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs11130114	0.80[EUR][1000 genomes]
rs11130115	0.92[CEU][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes]
rs11130123	0.86[TSI][hapmap]
rs11130124	0.81[CEU][hapmap];0.89[TSI][hapmap]
rs11707736	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11708451	0.80[EUR][1000 genomes]
rs11709660	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11712716	0.80[EUR][1000 genomes]
rs11713693	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11714373	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11715121	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11716539	0.80[EUR][1000 genomes]
rs11719738	0.87[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];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11917361	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11917474	0.81[EUR][1000 genomes]
rs11923706	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12493425	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12629262	0.80[EUR][1000 genomes]
rs12631730	0.90[CHB][hapmap];0.95[CHD][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs12715421	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13061071	0.92[CEU][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs13062022	0.80[EUR][1000 genomes]
rs13062681	0.85[EUR][1000 genomes]
rs13066214	0.82[EUR][1000 genomes]
rs13077398	0.81[EUR][1000 genomes]
rs13084117	0.80[EUR][1000 genomes]
rs13091054	0.89[EUR][1000 genomes]
rs13094438	0.81[CEU][hapmap];0.88[TSI][hapmap]
rs13098228	0.83[EUR][1000 genomes]
rs1466740	0.84[AFR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1466741	0.96[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17784127	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1811652	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1869869	0.81[EUR][1000 genomes]
rs2061197	0.91[ASW][hapmap];0.89[CEU][hapmap];0.91[TSI][hapmap];0.91[YRI][hapmap]
rs2132173	0.92[CEU][hapmap];0.88[TSI][hapmap]
rs2276853	0.81[CEU][hapmap];0.85[GIH][hapmap];0.89[TSI][hapmap]
rs2276854	0.81[CEU][hapmap];0.89[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];1.00[LWK][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2305634	0.92[CEU][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs2305635	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2305638	0.84[CEU][hapmap];0.80[EUR][1000 genomes]
rs2385867	0.84[EUR][1000 genomes]
rs34103310	0.89[EUR][1000 genomes]
rs34344887	0.82[EUR][1000 genomes]
rs4018905	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4078466	0.89[CEU][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs4082155	0.89[CEU][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs4234465	0.89[CEU][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs4682831	0.81[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];0.80[EUR][1000 genomes]
rs4683296	0.91[YRI][hapmap]
rs4683297	0.83[ASW][hapmap];0.91[YRI][hapmap]
rs55724164	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55843455	0.81[EUR][1000 genomes]
rs55927279	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56217494	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56249396	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57756484	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58956475	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61729713	0.81[EUR][1000 genomes]
rs62246375	0.81[EUR][1000 genomes]
rs62246398	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62246402	0.81[AFR][1000 genomes]
rs62246451	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62246455	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62248905	0.82[AFR][1000 genomes]
rs6414435	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6414436	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6442055	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6442059	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6442060	0.84[ASN][1000 genomes]
rs66539935	0.81[EUR][1000 genomes]
rs6763236	0.91[EUR][1000 genomes]
rs6766230	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6767218	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[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];1.00[LWK][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6768722	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6772670	0.95[CEU][hapmap];0.80[EUR][1000 genomes]
rs6773521	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6777145	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6781941	0.87[AFR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6785790	0.81[EUR][1000 genomes]
rs6791062	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6791842	0.81[CEU][hapmap]
rs6794193	0.90[EUR][1000 genomes]
rs7373821	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7426969	0.89[AMR][1000 genomes];0.89[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];1.00[LWK][hapmap];0.93[MKK][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[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];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.91[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];0.87[LWK][hapmap];0.91[MKK][hapmap];0.83[TSI][hapmap];0.91[YRI][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7610620	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7610636	0.85[EUR][1000 genomes]
rs7620997	0.88[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7621911	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs7623888	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7625067	0.91[EUR][1000 genomes]
rs7625070	0.91[EUR][1000 genomes]
rs7628747	0.89[CEU][hapmap];0.89[TSI][hapmap]
rs7632501	0.82[AFR][1000 genomes]
rs7633435	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7633698	0.81[EUR][1000 genomes]
rs7636252	0.81[EUR][1000 genomes]
rs7637302	0.84[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];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9812878	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9818382	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9821119	0.87[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];1.00[LWK][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9843075	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9844122	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9845728	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9852082	0.86[YRI][hapmap]
rs9854790	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9858443	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9875235	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4683322	SETD2	Cis_1M	lymphoblastoid	RTeQTL
rs4683322	KLHL18	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47078000-47130600	Weak transcription	Stomach Mucosa	stomach
2	chr3:47078800-47101400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:47079400-47095800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr3:47079600-47123800	Weak transcription	Pancreas	Pancrea
5	chr3:47079600-47124200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:47079800-47095000	Weak transcription	HMEC	breast
7	chr3:47079800-47098000	Weak transcription	Aorta	Aorta
8	chr3:47079800-47124200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:47080000-47095200	Weak transcription	Fetal Brain Male	brain
10	chr3:47083000-47098000	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr3:47083000-47098000	Weak transcription	A549	lung
12	chr3:47083000-47098400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr3:47083000-47106400	Weak transcription	Colonic Mucosa	Colon
14	chr3:47083200-47097800	Weak transcription	Gastric	stomach
15	chr3:47083200-47098000	Weak transcription	Brain Germinal Matrix	brain
16	chr3:47083200-47098000	Weak transcription	Ovary	ovary
17	chr3:47083200-47098200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr3:47083200-47135200	Weak transcription	Small Intestine	intestine
19	chr3:47083400-47117200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr3:47083400-47138600	Weak transcription	Psoas Muscle	Psoas
21	chr3:47083800-47097600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr3:47083800-47097600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr3:47083800-47097800	Weak transcription	Fetal Brain Female	brain
24	chr3:47083800-47098000	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr3:47083800-47098200	Weak transcription	NHLF	lung
26	chr3:47084000-47098000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr3:47084200-47093800	Weak transcription	Esophagus	oesophagus
28	chr3:47084200-47094600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr3:47084200-47097800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr3:47084200-47097800	Weak transcription	Spleen	Spleen
31	chr3:47084200-47098000	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr3:47084200-47098000	Weak transcription	Stomach Smooth Muscle	stomach
33	chr3:47084200-47098200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr3:47084200-47098200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr3:47084200-47098200	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr3:47084200-47098200	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr3:47084200-47098400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr3:47084200-47102800	Weak transcription	HUVEC	blood vessel
39	chr3:47084400-47097800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr3:47084400-47104800	Weak transcription	Fetal Kidney	kidney
41	chr3:47084400-47116000	Weak transcription	Right Ventricle	heart
42	chr3:47084800-47097800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr3:47084800-47098000	Weak transcription	Fetal Lung	lung
44	chr3:47085200-47095000	Weak transcription	Osteobl	bone
45	chr3:47085400-47094800	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr3:47086400-47095200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr3:47086600-47093400	Weak transcription	Primary hematopoietic stem cells	blood
48	chr3:47086600-47093400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr3:47086600-47094600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr3:47086600-47094800	Weak transcription	HepG2	liver

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