Variant report

Variant	rs35060561
Chromosome Location	chr3:49255503-49255504
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 95 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10049462	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10154895	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10865954	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs11130184	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs1134043	0.93[CEU][hapmap]
rs11552724	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs11706052	1.00[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs11706189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11710247	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11713297	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11715581	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs11716445	0.92[CEU][hapmap]
rs11717524	0.92[ASN][1000 genomes]
rs11718982	0.88[EUR][1000 genomes]
rs11719220	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];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11720460	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11920267	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12490393	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs12493001	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12629759	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs12631989	0.87[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12637576	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs12715434	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13064780	0.86[ASN][1000 genomes]
rs13068038	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13072554	0.83[EUR][1000 genomes]
rs13077498	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13080725	0.81[EUR][1000 genomes]
rs13096406	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13321689	1.00[ASW][hapmap]
rs2117938	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2304442	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs2334958	0.97[ASN][1000 genomes]
rs28690891	0.81[AFR][1000 genomes]
rs3212	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs34326553	0.90[EUR][1000 genomes]
rs34343820	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34504524	0.81[EUR][1000 genomes]
rs34566463	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34580506	1.00[CEU][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs34784192	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34889065	0.81[EUR][1000 genomes]
rs35102816	0.81[EUR][1000 genomes]
rs35108630	0.84[EUR][1000 genomes]
rs35174559	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs35185152	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35218722	0.86[ASN][1000 genomes]
rs35283189	1.00[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs35673421	1.00[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs3923475	0.82[EUR][1000 genomes]
rs4279134	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4513485	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4521268	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4955410	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4955418	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs4955419	1.00[JPT][hapmap]
rs4955420	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs4955432	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs5030795	1.00[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs55921200	0.83[EUR][1000 genomes]
rs56306491	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs66991555	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs67286839	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6779394	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs67831908	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6784111	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs71324939	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73084135	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7432989	1.00[CHD][hapmap]
rs7626445	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7652746	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9311439	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9311440	1.00[ASW][hapmap];0.89[YRI][hapmap]
rs9814987	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9818758	0.85[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap]
rs9826085	1.00[ASW][hapmap]
rs9826525	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9828310	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9835439	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9837237	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9837625	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9840050	1.00[CHD][hapmap]
rs9844757	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap]
rs9846123	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9847839	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9850917	1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9855123	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9862483	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9870030	0.84[AMR][1000 genomes]
rs9873994	0.85[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap]
rs9880088	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9880309	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9990153	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834686	chr3:49106047-49270556	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	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:18)

SNP	Gene	Cis/trans	Tissue	Source
rs35060561	KBTBD3	trans	parietal	SCAN
rs35060561	WDR6	cis	Adipose Subcutaneous	GTEx
rs35060561	WDR6	cis	cerebellum	SCAN
rs35060561	WDR6	cis	Whole Blood	GTEx
rs35060561	WDR6	cis	Artery Tibial	GTEx
rs35060561	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs35060561	CCDC36	cis	cerebellum	SCAN
rs35060561	ARIH2	cis	cerebellum	SCAN
rs35060561	CSPG5	cis	parietal	SCAN
rs35060561	USP4	Cis_1M	lymphoblastoid	RTeQTL
rs35060561	NICN1	cis	cerebellum	SCAN
rs35060561	COL7A1	cis	parietal	SCAN
rs35060561	RNF123	cis	parietal	SCAN
rs35060561	ALAS1	cis	cerebellum	SCAN
rs35060561	WDR6	cis	Esophagus Mucosa	GTEx
rs35060561	C3orf62	cis	cerebellum	SCAN
rs35060561	WDR6	cis	parietal	SCAN
rs35060561	HEMK1	cis	parietal	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49237600-49255600	Weak transcription	Left Ventricle	heart
2	chr3:49250200-49274000	Weak transcription	Osteobl	bone
3	chr3:49251600-49265400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr3:49251800-49255600	Weak transcription	NHLF	lung
5	chr3:49252000-49265600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr3:49253200-49256600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr3:49255000-49256800	Enhancers	Fetal Muscle Leg	muscle
8	chr3:49255200-49255600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
9	chr3:49255200-49255800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr3:49255200-49255800	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr3:49255200-49255800	Enhancers	Aorta	Aorta
12	chr3:49255200-49255800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
13	chr3:49255200-49255800	Enhancers	Spleen	Spleen
14	chr3:49255200-49255800	Enhancers	HSMM	muscle
15	chr3:49255200-49255800	Enhancers	HSMMtube	muscle
16	chr3:49255200-49256000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr3:49255200-49256000	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr3:49255200-49256000	Enhancers	Esophagus	oesophagus
19	chr3:49255200-49256000	Enhancers	Psoas Muscle	Psoas
20	chr3:49255200-49256000	Enhancers	HMEC	breast
21	chr3:49255200-49256200	Enhancers	Brain Hippocampus Middle	brain
22	chr3:49255200-49256400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr3:49255200-49256400	Enhancers	Brain Substantia Nigra	brain
24	chr3:49255200-49256400	Enhancers	Fetal Stomach	stomach
25	chr3:49255200-49256600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr3:49255200-49256600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
27	chr3:49255200-49256600	Enhancers	Fetal Heart	heart
28	chr3:49255200-49256600	Enhancers	Pancreas	Pancrea
29	chr3:49255200-49256600	Enhancers	Hela-S3	cervix
30	chr3:49255200-49256800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr3:49255200-49256800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr3:49255200-49256800	Enhancers	Fetal Muscle Trunk	muscle
33	chr3:49255200-49256800	Enhancers	Ovary	ovary
34	chr3:49255200-49256800	Enhancers	Right Atrium	heart
35	chr3:49255200-49256800	Enhancers	HepG2	liver
36	chr3:49255200-49256800	Enhancers	HUVEC	blood vessel
37	chr3:49255200-49256800	Enhancers	NHDF-Ad	bronchial
38	chr3:49255200-49257000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr3:49255200-49257600	Enhancers	Rectal Smooth Muscle	rectum
40	chr3:49255200-49258000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr3:49255400-49255800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr3:49255400-49255800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr3:49255400-49255800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr3:49255400-49255800	Flanking Active TSS	Adipose Nuclei	Adipose
45	chr3:49255400-49255800	Enhancers	Brain Angular Gyrus	brain
46	chr3:49255400-49255800	Flanking Active TSS	Colon Smooth Muscle	Colon
47	chr3:49255400-49255800	Enhancers	Right Ventricle	heart
48	chr3:49255400-49256000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr3:49255400-49256000	Enhancers	Sigmoid Colon	Sigmoid Colon
50	chr3:49255400-49256200	Enhancers	Primary hematopoietic stem cells short term culture	blood

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