Variant report

Variant	rs12488225
Chromosome Location	chr3:47235107-47235108
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:47206313..47209230-chr3:47234534..47237007,2	K562	blood:
2	chr3:47212755..47215203-chr3:47233129..47236003,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KLHL18-6	chr3:47234969-47239512	NONHSAT089483

Extended variants
information (count: 108 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs1076394	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs1079276	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs10865946	0.89[CEU][hapmap]
rs11130114	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11130115	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11130123	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs11130124	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap]
rs11130126	0.81[CEU][hapmap]
rs11708451	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11710013	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs11710322	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs11712445	0.88[CEU][hapmap]
rs11712716	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11714282	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11714373	0.86[EUR][1000 genomes]
rs11716539	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11718795	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11719306	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11719738	0.87[EUR][1000 genomes]
rs11719877	0.88[CEU][hapmap]
rs11720139	0.92[CEU][hapmap]
rs11915074	0.82[CEU][hapmap]
rs11920853	0.82[CEU][hapmap]
rs11923706	0.82[EUR][1000 genomes]
rs12489211	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12493425	0.87[EUR][1000 genomes]
rs12629262	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12635619	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13061071	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13062022	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13063250	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13075233	0.88[CEU][hapmap]
rs13078131	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13084117	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13091054	0.81[EUR][1000 genomes]
rs13094438	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13094672	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13098228	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1466740	0.84[EUR][1000 genomes]
rs1466741	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs1638676	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs17411375	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs17784127	0.88[CEU][hapmap]
rs1811652	0.87[EUR][1000 genomes]
rs1872164	0.88[CEU][hapmap]
rs2132173	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2159400	0.88[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap]
rs2276853	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2276854	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2278963	0.92[CEU][hapmap]
rs2305634	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2305635	0.92[CEU][hapmap]
rs2305638	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs295428	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs295441	0.89[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs295442	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs295449	0.88[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs295458	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs295461	0.88[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap]
rs4018905	0.84[EUR][1000 genomes]
rs4078466	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.82[EUR][1000 genomes]
rs4082155	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs4682852	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4683320	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4683322	0.92[CEU][hapmap]
rs4683324	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4683326	0.88[CEU][hapmap];0.87[YRI][hapmap]
rs4858824	0.88[CEU][hapmap]
rs57756484	0.89[EUR][1000 genomes]
rs58956475	0.86[EUR][1000 genomes]
rs62246451	0.87[EUR][1000 genomes]
rs62246455	0.90[EUR][1000 genomes]
rs6414436	0.81[EUR][1000 genomes]
rs6442059	0.87[EUR][1000 genomes]
rs6763236	0.81[EUR][1000 genomes]
rs6766230	0.87[EUR][1000 genomes]
rs6767907	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs6768221	0.82[CEU][hapmap]
rs6772670	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6773521	0.90[EUR][1000 genomes]
rs6781941	0.88[EUR][1000 genomes]
rs6785790	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6791062	0.85[EUR][1000 genomes]
rs6791842	0.89[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.92[YRI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6794193	0.82[EUR][1000 genomes]
rs7433300	0.83[CEU][hapmap]
rs749511	0.92[CEU][hapmap]
rs749512	0.88[CEU][hapmap]
rs7615323	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7621911	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7625067	0.81[EUR][1000 genomes]
rs7625070	0.81[EUR][1000 genomes]
rs807932	0.84[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs807936	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs811115	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs922957	0.89[CEU][hapmap]
rs9311403	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs9818382	0.87[EUR][1000 genomes]
rs9821119	0.87[EUR][1000 genomes]
rs9837343	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs9843075	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv590211	chr3:47189485-47256057	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv3801	chr3:47201530-47246438	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv1014457	chr3:47222292-47335175	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv536560	chr3:47222292-47335175	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	esv3343630	chr3:47232548-47238746	Weak transcription ZNF genes & repeats Strong transcription Enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12488225	SETD2	Cis_1M	lymphoblastoid	RTeQTL
rs12488225	RTP3	cis	lesional skin	skin_eQTL
rs12488225	KLHL18	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47207000-47253800	Weak transcription	Aorta	Aorta
2	chr3:47207200-47235800	Weak transcription	Primary hematopoietic stem cells	blood
3	chr3:47208000-47249600	Weak transcription	Ovary	ovary
4	chr3:47208200-47256400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr3:47208200-47276600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr3:47217800-47236600	Weak transcription	Right Ventricle	heart
7	chr3:47219400-47243400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr3:47221000-47250200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr3:47221400-47236000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr3:47222600-47244200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr3:47222800-47235400	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr3:47222800-47236800	Weak transcription	Left Ventricle	heart
13	chr3:47222800-47249000	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr3:47222800-47249400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:47223000-47236400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr3:47223200-47235200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr3:47223200-47240200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr3:47223400-47242800	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr3:47223400-47245200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr3:47223400-47256600	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr3:47223800-47252600	Weak transcription	Fetal Muscle Leg	muscle
22	chr3:47223800-47269200	Weak transcription	Fetal Muscle Trunk	muscle
23	chr3:47224200-47250200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr3:47228400-47240000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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