Variant report

Variant	rs4955417
Chromosome Location	chr3:49298205-49298206
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 31 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10154992	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10155014	1.00[ASN][1000 genomes]
rs11130183	0.88[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];0.92[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11130186	0.88[ASW][hapmap];0.91[CEU][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11130187	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11710434	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11719762	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11720542	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11720657	0.86[CEU][hapmap]
rs12637346	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13096474	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];1.00[ASN][1000 genomes]
rs1464569	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];1.00[ASN][1000 genomes]
rs17080510	1.00[CHB][hapmap]
rs2082923	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2099526	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2140270	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap]
rs2177268	1.00[CEU][hapmap]
rs2329025	1.00[ASN][1000 genomes]
rs3448	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap]
rs3870339	1.00[ASN][1000 genomes]
rs3905330	1.00[ASN][1000 genomes]
rs4052546	1.00[ASN][1000 genomes]
rs4292260	0.91[CEU][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.81[YRI][hapmap]
rs4384984	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4855858	1.00[ASN][1000 genomes]
rs4955411	0.91[CEU][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.81[YRI][hapmap]
rs4955414	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4955416	0.86[CEU][hapmap];0.84[MEX][hapmap];0.81[YRI][hapmap]
rs4955421	0.96[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4955423	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4955426	0.91[CEU][hapmap]
rs4955427	0.91[EUR][1000 genomes]
rs4955430	1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];0.81[MKK][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes]
rs4955439	0.95[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4955443	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57273516	1.00[ASN][1000 genomes]
rs6446256	1.00[CEU][hapmap];0.96[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6446257	0.95[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6769744	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6769821	0.95[CEU][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs6778080	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6805609	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap]
rs6808036	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6809204	0.83[EUR][1000 genomes]
rs6809851	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7429661	0.95[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes]
rs7432077	0.81[EUR][1000 genomes]
rs7617480	1.00[GIH][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap]
rs7619016	1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7619789	1.00[ASN][1000 genomes]
rs7620024	1.00[ASN][1000 genomes]
rs7626076	1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7631586	0.88[EUR][1000 genomes]
rs8897	1.00[CEU][hapmap]
rs940045	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];1.00[ASN][1000 genomes]
rs9586	1.00[GIH][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap]
rs974495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9757181	1.00[CEU][hapmap]
rs9831648	1.00[GIH][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap]
rs9834003	0.88[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9860285	0.82[EUR][1000 genomes]
rs9865051	0.91[CEU][hapmap]
rs9867285	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9881860	1.00[CEU][hapmap];0.82[EUR][1000 genomes]

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:31)

SNP	Gene	Cis/trans	Tissue	Source
rs4955417	NICN1	cis	Thyroid	GTEx
rs4955417	AMT	cis	Muscle Skeletal	GTEx
rs4955417	WDR6	cis	Muscle Skeletal	GTEx
rs4955417	AMT	cis	lung	GTEx
rs4955417	AMT	cis	Esophagus Mucosa	GTEx
rs4955417	AMT	cis	cerebellum	SCAN
rs4955417	ARIH2	cis	Thyroid	GTEx
rs4955417	P4HTM	cis	parietal	SCAN
rs4955417	WDR6	cis	Heart Left Ventricle	GTEx
rs4955417	AMT	Cis_1M	lymphoblastoid	RTeQTL
rs4955417	PFKFB4	cis	Nerve Tibial	GTEx
rs4955417	NICN1-AS1	cis	Thyroid	GTEx
rs4955417	QRICH1	cis	cerebellum	SCAN
rs4955417	ZNF589	cis	parietal	SCAN
rs4955417	GMPPB	cis	parietal	SCAN
rs4955417	WDR6	cis	cerebellum	SCAN
rs4955417	AMT	cis	Artery Aorta	GTEx
rs4955417	AMT	cis	Adipose Subcutaneous	GTEx
rs4955417	WDR6	cis	Nerve Tibial	GTEx
rs4955417	NCKIPSD	cis	Esophagus Muscularis	GTEx
rs4955417	GPX1	cis	parietal	SCAN
rs4955417	DALRD3	cis	cerebellum	SCAN
rs4955417	AMT	cis	Nerve Tibial	GTEx
rs4955417	AMT	cis	Thyroid	GTEx
rs4955417	WDR6	cis	parietal	SCAN
rs4955417	SEMA3G	cis	cerebellum	SCAN
rs4955417	AMT	cis	Artery Tibial	GTEx
rs4955417	AMT	cis	Whole Blood	GTEx
rs4955417	DALRD3	cis	parietal	SCAN
rs4955417	NICN1	cis	cerebellum	SCAN
rs4955417	AMT	cis	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49276400-49306400	Weak transcription	Spleen	Spleen
2	chr3:49276600-49304000	Weak transcription	Stomach Smooth Muscle	stomach
3	chr3:49282600-49299000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:49282600-49303200	Weak transcription	Left Ventricle	heart
5	chr3:49286400-49304000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr3:49286400-49313600	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr3:49290600-49303400	Weak transcription	Brain Angular Gyrus	brain
8	chr3:49292800-49306800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr3:49293000-49313400	Weak transcription	HSMM	muscle
10	chr3:49293600-49304000	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr3:49293600-49306400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr3:49293800-49305400	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr3:49293800-49306400	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr3:49293800-49307000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr3:49293800-49308400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr3:49294000-49306600	Weak transcription	Placenta	Placenta
17	chr3:49294000-49308400	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr3:49294200-49303400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr3:49294400-49304000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr3:49294600-49303200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr3:49294600-49303400	Weak transcription	Fetal Muscle Leg	muscle
22	chr3:49294600-49304000	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr3:49294800-49303200	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr3:49294800-49306800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr3:49294800-49313400	Weak transcription	NHLF	lung
26	chr3:49295000-49303400	Weak transcription	Fetal Muscle Trunk	muscle
27	chr3:49295000-49303400	Weak transcription	Rectal Smooth Muscle	rectum
28	chr3:49295000-49303400	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr3:49295000-49304000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr3:49295000-49304000	Weak transcription	Fetal Stomach	stomach
31	chr3:49295000-49304200	Weak transcription	Osteobl	bone
32	chr3:49295000-49306600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr3:49295000-49313200	Weak transcription	Right Ventricle	heart
34	chr3:49295400-49298400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr3:49297400-49299600	Enhancers	Fetal Intestine Large	intestine
36	chr3:49297600-49299400	Enhancers	Duodenum Mucosa	Duodenum
37	chr3:49297600-49299600	Enhancers	Fetal Intestine Small	intestine
38	chr3:49297800-49298400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr3:49297800-49299400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr3:49298000-49298400	Enhancers	Adipose Nuclei	Adipose
41	chr3:49298000-49299400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
42	chr3:49298200-49298400	Enhancers	Lung	lung
43	chr3:49298200-49298600	Flanking Active TSS	HepG2	liver

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