Variant report

Variant	rs12631989
Chromosome Location	chr3:49273996-49273997
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KLHDC8B-1	chr3:49273981-49274007	NONHSAT089684

Extended variants
information (count: 76 )
Associated
traits (count: 36 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10049462	1.00[JPT][hapmap]
rs10865954	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap]
rs11130184	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11130185	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11552724	1.00[JPT][hapmap]
rs11706189	1.00[JPT][hapmap]
rs11710247	0.92[ASN][1000 genomes]
rs11713297	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs11715581	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11716334	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11717524	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11719220	0.87[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11720460	0.92[ASN][1000 genomes]
rs11920267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12490393	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12493001	0.92[CEU][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap]
rs12629637	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12629759	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12637576	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13064780	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13068038	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs13077498	1.00[JPT][hapmap]
rs1865741	0.82[CEU][hapmap]
rs2117938	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2304442	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2334958	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3212	0.92[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap]
rs34566463	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs34580506	1.00[JPT][hapmap]
rs34784192	0.92[ASN][1000 genomes]
rs35060561	0.87[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs35174559	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35185152	0.86[ASN][1000 genomes]
rs35218722	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35283189	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs35673421	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs3774800	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap]
rs4279134	0.92[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap]
rs4308307	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4367098	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4499638	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4513485	0.84[ASW][hapmap];0.92[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap]
rs4521268	0.92[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs4536858	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4955410	0.84[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.86[YRI][hapmap]
rs4955418	0.96[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4955419	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs4955420	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap]
rs4955432	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5030795	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs55713230	0.91[EUR][1000 genomes]
rs57245267	0.83[AFR][1000 genomes]
rs67286839	0.92[ASN][1000 genomes]
rs6779394	0.92[CEU][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap]
rs6784111	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs6794924	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6795756	0.89[EUR][1000 genomes]
rs6795772	0.82[CEU][hapmap];0.87[LWK][hapmap];0.87[MKK][hapmap]
rs71324939	0.95[ASN][1000 genomes]
rs7432989	0.88[CEU][hapmap];0.87[CHD][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs7626445	0.88[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs7638154	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7652746	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.85[MKK][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9311439	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9814987	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs9826525	0.92[ASN][1000 genomes]
rs9837237	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs9837625	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs9840050	0.88[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];0.83[TSI][hapmap]
rs9846123	0.88[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs9847839	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs9850917	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9880088	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs9880309	1.00[JPT][hapmap]
rs9990153	0.87[CHD][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008750	chr3:49208815-49362401	Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:36)

SNP	Gene	Cis/trans	Tissue	Source
rs12631989	WDR6	cis	lymphoblastoid	seeQTL
rs12631989	CCDC36	cis	Esophagus Muscularis	GTEx
rs12631989	WDR6	cis	Artery Tibial	GTEx
rs12631989	P4HTM	cis	cerebellum	SCAN
rs12631989	NCKIPSD	cis	parietal	SCAN
rs12631989	WDR6	cis	cerebellum	SCAN
rs12631989	NCKIPSD	cis	Esophagus Muscularis	GTEx
rs12631989	AMT	cis	cerebellum	SCAN
rs12631989	C3orf62	cis	cerebellum	SCAN
rs12631989	WDR6	cis	Esophagus Muscularis	GTEx
rs12631989	ZNF589	cis	parietal	SCAN
rs12631989	CCDC36	cis	Artery Tibial	GTEx
rs12631989	NICN1-AS1	cis	Thyroid	GTEx
rs12631989	AMT	cis	Artery Aorta	GTEx
rs12631989	WDR6	cis	Whole Blood	GTEx
rs12631989	PH-4	Cis_1M	lymphoblastoid	RTeQTL
rs12631989	AMT	cis	parietal	SCAN
rs12631989	AMT	cis	lung	GTEx
rs12631989	WDR6	cis	Muscle Skeletal	GTEx
rs12631989	TLR9	cis	parietal	SCAN
rs12631989	AMT	cis	Whole Blood	GTEx
rs12631989	WDR6	cis	Esophagus Mucosa	GTEx
rs12631989	WDR6	cis	Nerve Tibial	GTEx
rs12631989	SEMA3G	cis	cerebellum	SCAN
rs12631989	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs12631989	CXorf38	trans	parietal	SCAN
rs12631989	WDR6	cis	parietal	SCAN
rs12631989	WDR6	cis	lung	GTEx
rs12631989	NCKIPSD	cis	cerebellum	SCAN
rs12631989	NICN1	cis	Thyroid	GTEx
rs12631989	WDR6	cis	Adipose Subcutaneous	GTEx
rs12631989	DALRD3	cis	cerebellum	SCAN
rs12631989	P4HTM	cis	parietal	SCAN
rs12631989	CCDC71	cis	cerebellum	SCAN
rs12631989	AMT	cis	Thyroid	GTEx
rs12631989	AMT	cis	Muscle Skeletal	GTEx

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49250200-49274000	Weak transcription	Osteobl	bone
2	chr3:49256600-49275800	Weak transcription	NHLF	lung
3	chr3:49266200-49292600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr3:49270200-49283000	Weak transcription	Ovary	ovary
5	chr3:49271600-49275400	Weak transcription	Aorta	Aorta
6	chr3:49271600-49275600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr3:49272200-49275400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr3:49272200-49275400	Weak transcription	Adipose Nuclei	Adipose
9	chr3:49272200-49276000	Weak transcription	Fetal Heart	heart
10	chr3:49272400-49275400	Weak transcription	Fetal Muscle Leg	muscle
11	chr3:49272400-49275800	Weak transcription	Fetal Muscle Trunk	muscle
12	chr3:49272400-49277000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr3:49272600-49275400	Weak transcription	Fetal Stomach	stomach
14	chr3:49273800-49274400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr3:49273800-49275000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr3:49273800-49276000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr3:49273800-49278400	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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