Variant report

Variant	rs3905330
Chromosome Location	chr3:49550774-49550775
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	chr3:49541500..49543859-chr3:49548888..49551705,2	K562	blood:

Extended variants
information (count: 97 )
Associated
traits (count: 35 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs1009051	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10155014	0.86[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10452032	1.00[CHD][hapmap];0.91[MKK][hapmap]
rs1078341	1.00[CHD][hapmap];0.92[MKK][hapmap]
rs10865956	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1106620	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11130204	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11130208	1.00[CHD][hapmap];0.83[LWK][hapmap];0.89[MKK][hapmap]
rs11130211	1.00[CHB][hapmap]
rs11130217	1.00[CHD][hapmap];0.92[MKK][hapmap]
rs11709734	1.00[CHD][hapmap]
rs11715060	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs11719762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11720657	0.86[CEU][hapmap]
rs11923032	0.83[AFR][1000 genomes]
rs11928090	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12583	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12637313	1.00[CHD][hapmap]
rs13096474	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13322887	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1352889	1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[LWK][hapmap];0.95[MKK][hapmap]
rs1464569	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1491983	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[LWK][hapmap];0.95[MKK][hapmap]
rs1982861	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2029591	1.00[CHD][hapmap];0.92[MKK][hapmap]
rs2131108	1.00[CHD][hapmap];0.92[MKK][hapmap]
rs2140270	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs2177268	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs2312462	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2329021	1.00[CHD][hapmap];0.92[MKK][hapmap]
rs2329025	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3448	1.00[CEU][hapmap];1.00[GIH][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap]
rs34890793	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap]
rs3866330	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3870339	0.95[CEU][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3870341	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4052546	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4241405	1.00[CHD][hapmap];0.92[MKK][hapmap]
rs4241407	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855833	1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[LWK][hapmap];0.95[MKK][hapmap]
rs4855837	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4855846	1.00[CHD][hapmap];0.92[MKK][hapmap]
rs4855853	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4855858	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855869	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4855882	1.00[CHD][hapmap]
rs4855885	1.00[CHD][hapmap]
rs4955417	1.00[ASN][1000 genomes]
rs4955430	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap]
rs56049603	0.82[EUR][1000 genomes]
rs56127630	0.85[EUR][1000 genomes]
rs56324858	0.83[EUR][1000 genomes]
rs57273516	0.89[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62259933	0.89[EUR][1000 genomes]
rs62259943	0.84[EUR][1000 genomes]
rs62259944	0.81[EUR][1000 genomes]
rs62259947	0.85[EUR][1000 genomes]
rs62261183	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62261249	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6446275	0.89[EUR][1000 genomes]
rs6446285	1.00[CHD][hapmap]
rs6769744	0.82[AFR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6774202	1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[LWK][hapmap];0.94[MKK][hapmap]
rs6783003	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs6785045	0.85[EUR][1000 genomes]
rs6805609	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes]
rs72934271	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73088137	0.86[EUR][1000 genomes]
rs7355800	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7374731	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7613491	0.93[EUR][1000 genomes]
rs7619789	0.86[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7620024	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7622786	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7625857	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7638750	0.81[EUR][1000 genomes]
rs7644148	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7647973	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs7648995	0.85[EUR][1000 genomes]
rs7651372	0.93[EUR][1000 genomes]
rs7653505	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[LWK][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs8897	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.88[EUR][1000 genomes]
rs940045	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9654010	0.87[EUR][1000 genomes]
rs974495	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9757181	1.00[CEU][hapmap];0.80[AFR][1000 genomes]
rs9809237	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9817807	0.84[EUR][1000 genomes]
rs9824435	1.00[CHD][hapmap]
rs9842132	0.84[EUR][1000 genomes]
rs9860055	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9861027	0.85[EUR][1000 genomes]
rs9862534	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9871024	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9881860	1.00[CEU][hapmap]
rs9883000	1.00[CHD][hapmap];0.92[MKK][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	nsv834687	chr3:49448632-49631788	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:35)

SNP	Gene	Cis/trans	Tissue	Source
rs3905330	WDR6	cis	Esophagus Muscularis	GTEx
rs3905330	WDR6	cis	Nerve Tibial	GTEx
rs3905330	AMT	cis	Esophagus Muscularis	GTEx
rs3905330	AMT	cis	Esophagus Mucosa	GTEx
rs3905330	NME6	cis	cerebellum	SCAN
rs3905330	GMPPB	cis	parietal	SCAN
rs3905330	AMT	cis	Nerve Tibial	GTEx
rs3905330	WDR6	cis	parietal	SCAN
rs3905330	NICN1	cis	cerebellum	SCAN
rs3905330	AMT	cis	parietal	SCAN
rs3905330	AMT	cis	lung	GTEx
rs3905330	GPX1	cis	parietal	SCAN
rs3905330	AMT	cis	Artery Tibial	GTEx
rs3905330	WDR6	cis	Muscle Skeletal	GTEx
rs3905330	GNL3	cis	cerebellum	SCAN
rs3905330	NCKIPSD	cis	Esophagus Muscularis	GTEx
rs3905330	AMT	cis	Artery Aorta	GTEx
rs3905330	AMT	cis	Skin Sun Exposed Lower leg	GTEx
rs3905330	DALRD3	cis	parietal	SCAN
rs3905330	SEMA3G	cis	cerebellum	SCAN
rs3905330	AMT	cis	Muscle Skeletal	GTEx
rs3905330	AMT	cis	Whole Blood	GTEx
rs3905330	AMT	cis	Adipose Subcutaneous	GTEx
rs3905330	ZNF589	cis	parietal	SCAN
rs3905330	AMT	cis	Thyroid	GTEx
rs3905330	NICN1-AS1	cis	Thyroid	GTEx
rs3905330	NICN1	cis	Thyroid	GTEx
rs3905330	DALRD3	cis	cerebellum	SCAN
rs3905330	WDR6	cis	cerebellum	SCAN
rs3905330	P4HTM	cis	parietal	SCAN
rs3905330	AMT	Cis_1M	lymphoblastoid	RTeQTL
rs3905330	QRICH1	cis	cerebellum	SCAN
rs3905330	AMT	cis	cerebellum	SCAN
rs3905330	WDR6	cis	lung	GTEx
rs3905330	LZTFL1	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49529600-49568600	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr3:49538000-49554800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:49538800-49553800	Weak transcription	HUVEC	blood vessel
4	chr3:49538800-49554200	Weak transcription	Aorta	Aorta
5	chr3:49539600-49568600	Weak transcription	Small Intestine	intestine
6	chr3:49542000-49553200	Weak transcription	A549	lung
7	chr3:49546200-49577000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr3:49546400-49554400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr3:49546600-49552000	Strong transcription	Hela-S3	cervix
10	chr3:49546600-49556200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr3:49546600-49556400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr3:49547000-49572000	Weak transcription	Fetal Brain Male	brain
13	chr3:49547400-49552000	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr3:49547400-49562200	Strong transcription	Primary T cells from cord blood	blood
15	chr3:49547600-49555400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
16	chr3:49547600-49556000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:49547600-49556200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr3:49547600-49564200	Strong transcription	Fetal Intestine Small	intestine
19	chr3:49547800-49551200	Strong transcription	H9 Cell Line	embryonic stem cell
20	chr3:49547800-49551200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr3:49547800-49551200	Strong transcription	Brain Inferior Temporal Lobe	brain
22	chr3:49547800-49551200	Strong transcription	HSMMtube	muscle
23	chr3:49547800-49551400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr3:49547800-49551400	Strong transcription	Brain Germinal Matrix	brain
25	chr3:49547800-49551400	Strong transcription	Rectal Mucosa Donor 31	rectum
26	chr3:49547800-49551400	Strong transcription	Thymus	Thymus
27	chr3:49547800-49551600	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr3:49547800-49551600	Strong transcription	GM12878-XiMat	blood
29	chr3:49547800-49551600	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr3:49547800-49552000	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr3:49547800-49552000	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr3:49547800-49552200	Strong transcription	H1 Cell Line	embryonic stem cell
33	chr3:49547800-49552200	Strong transcription	Dnd41	blood
34	chr3:49547800-49553400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr3:49547800-49554800	Strong transcription	Fetal Muscle Leg	muscle
36	chr3:49547800-49555000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr3:49547800-49555800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr3:49547800-49556200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr3:49547800-49556200	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr3:49547800-49556400	Strong transcription	Primary B cells from peripheral blood	blood
41	chr3:49547800-49557200	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr3:49547800-49557800	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr3:49547800-49558000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
44	chr3:49547800-49559000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr3:49547800-49560400	Strong transcription	Fetal Thymus	thymus
46	chr3:49547800-49562800	Strong transcription	Fetal Stomach	stomach
47	chr3:49548000-49551200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
48	chr3:49548000-49551200	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr3:49548000-49551200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr3:49548000-49551400	Strong transcription	Primary B cells from cord blood	blood

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