Variant report

Variant	rs12493425
Chromosome Location	chr3:47176946-47176947
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:47175740..47177368-chr3:47181984..47183489,2	K562	blood:
2	chr3:47175569..47177603-chr3:47199664..47202518,2	K562	blood:

Extended variants
information (count: 101 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs10433549	0.87[ASN][1000 genomes]
rs11130114	0.91[EUR][1000 genomes]
rs11130115	0.91[EUR][1000 genomes]
rs11707736	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11708451	0.91[EUR][1000 genomes]
rs11709660	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11712716	0.91[EUR][1000 genomes]
rs11713693	0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs11714282	0.82[EUR][1000 genomes]
rs11714373	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11715121	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11716539	0.91[EUR][1000 genomes]
rs11718795	0.90[EUR][1000 genomes]
rs11719306	0.91[EUR][1000 genomes]
rs11719738	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11720139	0.88[ASN][1000 genomes]
rs11917361	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11920354	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11923706	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11925560	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12488225	0.87[EUR][1000 genomes]
rs12489211	0.88[EUR][1000 genomes]
rs12629262	0.91[EUR][1000 genomes]
rs12631730	0.84[ASN][1000 genomes]
rs12635619	0.88[EUR][1000 genomes]
rs12715421	0.86[AFR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13061071	0.87[EUR][1000 genomes]
rs13062022	0.91[EUR][1000 genomes]
rs13078131	0.82[EUR][1000 genomes]
rs13084117	0.91[EUR][1000 genomes]
rs13094672	0.88[EUR][1000 genomes]
rs13098228	0.87[EUR][1000 genomes]
rs1466740	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1466741	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17784127	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1811652	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2088135	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2132173	0.84[EUR][1000 genomes]
rs2278963	0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2305635	0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs4018905	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4078466	0.81[EUR][1000 genomes]
rs4082155	0.81[EUR][1000 genomes]
rs4682852	0.91[EUR][1000 genomes]
rs4683320	0.91[EUR][1000 genomes]
rs4683322	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4683324	0.83[EUR][1000 genomes]
rs55724164	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55927279	0.91[ASN][1000 genomes]
rs56217494	0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs56249396	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56250009	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs57756484	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58956475	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59299766	0.82[ASN][1000 genomes]
rs62246398	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62246402	0.81[AFR][1000 genomes]
rs62246451	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62246455	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62248905	0.81[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs6414435	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6414436	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6442055	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6442059	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6442060	0.88[ASN][1000 genomes]
rs6766230	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6767218	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6767907	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6768722	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6772670	0.91[EUR][1000 genomes]
rs6773521	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6777145	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6781941	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6785790	0.88[EUR][1000 genomes]
rs6791062	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6794193	0.80[EUR][1000 genomes]
rs7373821	0.85[ASN][1000 genomes]
rs7433300	0.91[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs749511	0.88[ASN][1000 genomes]
rs749512	0.88[ASN][1000 genomes]
rs7610620	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7615323	0.87[EUR][1000 genomes]
rs7620997	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7621911	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs7623888	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7632501	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7633435	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9311403	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9812878	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9818382	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9821119	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9837343	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9843075	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9844122	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9845728	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9854790	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9858443	0.86[AFR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9875235	0.88[AFR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]

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	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
2	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
3	nsv590210	chr3:47126543-47214122	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12493425	KLHL18	Cis_1M	lymphoblastoid	RTeQTL
rs12493425	SETD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47155400-47183800	Weak transcription	Esophagus	oesophagus
2	chr3:47165800-47177200	Weak transcription	Brain Hippocampus Middle	brain
3	chr3:47165800-47187000	Weak transcription	Stomach Smooth Muscle	stomach
4	chr3:47165800-47191000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr3:47165800-47197000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:47166000-47177000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr3:47166000-47177200	Weak transcription	Colon Smooth Muscle	Colon
8	chr3:47166000-47177200	Weak transcription	Ovary	ovary
9	chr3:47166000-47177400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr3:47166000-47177600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:47166000-47178200	Weak transcription	Placenta	Placenta
12	chr3:47166000-47180600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr3:47166000-47180600	Weak transcription	Adipose Nuclei	Adipose
14	chr3:47166000-47180800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr3:47166000-47181400	Weak transcription	A549	lung
16	chr3:47166000-47181600	Weak transcription	Fetal Intestine Large	intestine
17	chr3:47166000-47181800	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr3:47166000-47182000	Weak transcription	Lung	lung
19	chr3:47166000-47182000	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr3:47166000-47182600	Weak transcription	Fetal Lung	lung
21	chr3:47166000-47182800	Weak transcription	Rectal Smooth Muscle	rectum
22	chr3:47166000-47183000	Weak transcription	Fetal Kidney	kidney
23	chr3:47166000-47200800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr3:47166000-47201200	Weak transcription	Fetal Muscle Leg	muscle
25	chr3:47166000-47204600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr3:47166200-47197200	Weak transcription	Aorta	Aorta
27	chr3:47166200-47200600	Weak transcription	Hela-S3	cervix
28	chr3:47166400-47194200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr3:47166600-47182800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr3:47166600-47204200	Weak transcription	Fetal Muscle Trunk	muscle
31	chr3:47167200-47182000	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr3:47167400-47202400	Weak transcription	HSMM	muscle
33	chr3:47167800-47181800	Weak transcription	Fetal Intestine Small	intestine
34	chr3:47167800-47187600	Weak transcription	Fetal Stomach	stomach
35	chr3:47167800-47195400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr3:47170000-47177400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr3:47170000-47182000	Weak transcription	Pancreas	Pancrea
38	chr3:47170200-47182800	Weak transcription	Dnd41	blood
39	chr3:47170200-47183600	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr3:47171000-47177600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr3:47171200-47177400	Weak transcription	Brain Anterior Caudate	brain
42	chr3:47171600-47177600	Weak transcription	Brain Substantia Nigra	brain
43	chr3:47171800-47181600	Weak transcription	GM12878-XiMat	blood
44	chr3:47172000-47177000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr3:47172600-47182000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr3:47172600-47183200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr3:47172800-47177000	Weak transcription	HMEC	breast
48	chr3:47173600-47191000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr3:47173800-47177200	Enhancers	Primary neutrophils fromperipheralblood	blood
50	chr3:47174800-47178400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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