Variant report

Variant	rs7625067
Chromosome Location	chr3:47095305-47095306
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 111 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10433549	0.81[EUR][1000 genomes]
rs10461018	0.86[EUR][1000 genomes]
rs1079276	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1108301	0.89[EUR][1000 genomes]
rs11130110	0.86[EUR][1000 genomes]
rs11130111	0.89[EUR][1000 genomes]
rs11130112	0.89[EUR][1000 genomes]
rs11130114	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11130115	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11707736	0.85[EUR][1000 genomes]
rs11708451	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11709660	0.89[EUR][1000 genomes]
rs11712716	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11714282	0.80[ASN][1000 genomes]
rs11715121	0.89[EUR][1000 genomes]
rs11716539	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11716553	0.84[EUR][1000 genomes]
rs11718795	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11719306	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11720139	0.82[EUR][1000 genomes]
rs11917361	0.89[EUR][1000 genomes]
rs11917474	0.89[EUR][1000 genomes]
rs12152493	0.88[EUR][1000 genomes]
rs12488225	0.81[EUR][1000 genomes]
rs12489211	0.84[EUR][1000 genomes]
rs12491473	0.86[EUR][1000 genomes]
rs12629262	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12630534	0.86[EUR][1000 genomes]
rs12635619	0.82[EUR][1000 genomes]
rs12715421	0.90[EUR][1000 genomes]
rs13061071	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13062022	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13062681	0.84[EUR][1000 genomes]
rs13066214	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13077398	0.89[EUR][1000 genomes]
rs13084117	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13087426	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13091054	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13094672	0.86[AFR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13098228	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1463393	0.86[EUR][1000 genomes]
rs17784127	0.83[EUR][1000 genomes]
rs1869869	0.89[EUR][1000 genomes]
rs1869871	0.81[EUR][1000 genomes]
rs2061197	0.85[EUR][1000 genomes]
rs2278963	0.83[EUR][1000 genomes]
rs2305634	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2305635	0.83[EUR][1000 genomes]
rs2305638	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2385867	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34103310	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34344887	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4018905	0.83[EUR][1000 genomes]
rs4078466	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4082155	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4234465	0.89[EUR][1000 genomes]
rs4682831	0.89[EUR][1000 genomes]
rs4682837	0.86[EUR][1000 genomes]
rs4682844	0.84[EUR][1000 genomes]
rs4682852	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4683320	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4683322	0.91[EUR][1000 genomes]
rs55724164	0.83[EUR][1000 genomes]
rs55843455	0.88[EUR][1000 genomes]
rs55927279	0.81[EUR][1000 genomes]
rs56249396	0.86[EUR][1000 genomes]
rs61729713	0.89[EUR][1000 genomes]
rs62246375	0.88[EUR][1000 genomes]
rs62246398	0.87[EUR][1000 genomes]
rs62248439	0.86[EUR][1000 genomes]
rs6414435	0.88[EUR][1000 genomes]
rs6414436	0.84[EUR][1000 genomes]
rs6442055	0.91[EUR][1000 genomes]
rs66539935	0.89[EUR][1000 genomes]
rs66564457	0.88[EUR][1000 genomes]
rs6763236	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6767218	0.86[EUR][1000 genomes]
rs6768722	0.88[EUR][1000 genomes]
rs6772670	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6774733	0.86[EUR][1000 genomes]
rs6777145	0.91[EUR][1000 genomes]
rs6785790	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6794193	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6808742	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7373821	0.82[EUR][1000 genomes]
rs7426969	0.81[EUR][1000 genomes]
rs749511	0.83[EUR][1000 genomes]
rs7610620	0.87[EUR][1000 genomes]
rs7610636	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7615323	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7617689	0.86[EUR][1000 genomes]
rs7621911	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7625070	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7628747	0.86[EUR][1000 genomes]
rs7633435	0.87[EUR][1000 genomes]
rs7633698	0.89[EUR][1000 genomes]
rs7636252	0.89[EUR][1000 genomes]
rs7637302	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7640397	0.86[EUR][1000 genomes]
rs9311403	0.83[EUR][1000 genomes]
rs9844122	0.90[EUR][1000 genomes]
rs9845728	0.90[EUR][1000 genomes]
rs9854790	0.91[EUR][1000 genomes]
rs9858443	0.90[EUR][1000 genomes]
rs9875235	0.89[EUR][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
rs7625067	KLHL18	Cis_1M	lymphoblastoid	RTeQTL
rs7625067	SETD2	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	chr3:47079800-47098000	Weak transcription	Aorta	Aorta
7	chr3:47079800-47124200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:47083000-47098000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr3:47083000-47098000	Weak transcription	A549	lung
10	chr3:47083000-47098400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr3:47083000-47106400	Weak transcription	Colonic Mucosa	Colon
12	chr3:47083200-47097800	Weak transcription	Gastric	stomach
13	chr3:47083200-47098000	Weak transcription	Brain Germinal Matrix	brain
14	chr3:47083200-47098000	Weak transcription	Ovary	ovary
15	chr3:47083200-47098200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr3:47083200-47135200	Weak transcription	Small Intestine	intestine
17	chr3:47083400-47117200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr3:47083400-47138600	Weak transcription	Psoas Muscle	Psoas
19	chr3:47083800-47097600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr3:47083800-47097600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr3:47083800-47097800	Weak transcription	Fetal Brain Female	brain
22	chr3:47083800-47098000	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr3:47083800-47098200	Weak transcription	NHLF	lung
24	chr3:47084000-47098000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr3:47084200-47097800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr3:47084200-47097800	Weak transcription	Spleen	Spleen
27	chr3:47084200-47098000	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr3:47084200-47098000	Weak transcription	Stomach Smooth Muscle	stomach
29	chr3:47084200-47098200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr3:47084200-47098200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr3:47084200-47098200	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr3:47084200-47098200	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr3:47084200-47098400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr3:47084200-47102800	Weak transcription	HUVEC	blood vessel
35	chr3:47084400-47097800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr3:47084400-47104800	Weak transcription	Fetal Kidney	kidney
37	chr3:47084400-47116000	Weak transcription	Right Ventricle	heart
38	chr3:47084800-47097800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr3:47084800-47098000	Weak transcription	Fetal Lung	lung
40	chr3:47086600-47095800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr3:47086600-47096800	Weak transcription	HSMMtube	muscle
42	chr3:47086600-47098000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr3:47086800-47096400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr3:47086800-47098000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr3:47086800-47098000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr3:47086800-47098000	Weak transcription	Adipose Nuclei	Adipose
47	chr3:47086800-47098000	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr3:47086800-47098000	Weak transcription	HSMM	muscle
49	chr3:47086800-47098200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr3:47087000-47096800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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