Variant report

Variant	rs4241407
Chromosome Location	chr3:49600319-49600320
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:49599253..49602377-chr3:49606582..49609679,3	K562	blood:
2	chr3:49599138..49600708-chr3:49694721..49696847,2	K562	blood:
3	chr3:49598309..49602377-chr3:49605664..49611011,5	K562	blood:

Extended variants
information (count: 103 )
Associated
traits (count: 38 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs1009051	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10155014	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10452032	0.82[ASW][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap];0.94[MKK][hapmap];0.95[YRI][hapmap]
rs1078341	0.82[ASW][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap];0.95[MKK][hapmap];0.95[YRI][hapmap]
rs10865956	1.00[ASW][hapmap];1.00[CEU][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];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1106620	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11130204	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11130207	0.93[AFR][1000 genomes]
rs11130208	0.91[ASW][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs11130211	1.00[CHB][hapmap];0.80[YRI][hapmap]
rs11130217	0.82[ASW][hapmap];1.00[CHD][hapmap];0.88[LWK][hapmap];0.95[MKK][hapmap];0.95[YRI][hapmap]
rs11709734	1.00[CHD][hapmap]
rs11719762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11720705	1.00[CHD][hapmap]
rs11928090	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12583	1.00[ASW][hapmap];1.00[CEU][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];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12637313	1.00[CHD][hapmap];0.95[YRI][hapmap]
rs12715437	0.82[ASW][hapmap];1.00[CHD][hapmap];0.88[LWK][hapmap];0.95[MKK][hapmap];0.95[YRI][hapmap]
rs13096474	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13096480	0.93[YRI][hapmap]
rs13322887	1.00[ASW][hapmap];1.00[CEU][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];0.95[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1352889	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[LWK][hapmap];0.92[MKK][hapmap];0.83[YRI][hapmap]
rs1464569	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1491983	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[LWK][hapmap];0.92[MKK][hapmap];0.83[YRI][hapmap]
rs1532204	0.97[AFR][1000 genomes]
rs1586827	0.95[YRI][hapmap]
rs1982861	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2029591	0.91[ASW][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap];0.95[MKK][hapmap];0.95[YRI][hapmap]
rs2131108	0.82[ASW][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap];0.95[MKK][hapmap];0.95[YRI][hapmap]
rs2140270	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.82[EUR][1000 genomes]
rs2177268	1.00[CEU][hapmap];0.95[YRI][hapmap];0.82[EUR][1000 genomes]
rs2312462	1.00[ASW][hapmap];1.00[CEU][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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2329021	0.82[ASW][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap];0.95[MKK][hapmap];0.95[YRI][hapmap]
rs2329025	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3020779	0.86[YRI][hapmap]
rs34890793	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[LWK][hapmap];0.89[MKK][hapmap]
rs3866330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3870339	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3870341	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3905330	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]
rs4052546	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4241405	0.91[ASW][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap];0.95[MKK][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes]
rs4855833	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[LWK][hapmap];0.92[MKK][hapmap];0.83[YRI][hapmap]
rs4855837	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4855838	0.84[AFR][1000 genomes]
rs4855845	0.95[YRI][hapmap]
rs4855846	0.82[ASW][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap];0.95[MKK][hapmap];0.95[YRI][hapmap]
rs4855853	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4855858	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855869	0.85[EUR][1000 genomes]
rs4855882	1.00[CHD][hapmap]
rs4855885	1.00[CHD][hapmap]
rs56049603	0.83[EUR][1000 genomes]
rs56127630	0.82[EUR][1000 genomes]
rs56324858	0.81[EUR][1000 genomes]
rs57273516	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62259933	0.86[EUR][1000 genomes]
rs62259943	0.80[EUR][1000 genomes]
rs62259947	0.82[EUR][1000 genomes]
rs62261183	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62261249	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6446275	0.86[EUR][1000 genomes]
rs6446284	0.87[AFR][1000 genomes]
rs6446285	1.00[CHD][hapmap]
rs6769744	1.00[ASN][1000 genomes]
rs6774202	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[LWK][hapmap];0.90[MKK][hapmap]
rs6783003	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6785045	0.82[EUR][1000 genomes]
rs6797299	1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs6805609	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs72934271	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73088137	0.83[EUR][1000 genomes]
rs7355800	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7374731	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7613491	0.90[EUR][1000 genomes]
rs7619789	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7620024	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7622786	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7625857	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7628207	1.00[CHD][hapmap]
rs7644148	1.00[ASW][hapmap];1.00[CEU][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];0.95[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7647973	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7648995	0.82[EUR][1000 genomes]
rs7651372	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7653505	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[MKK][hapmap]
rs8897	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.95[YRI][hapmap];0.84[EUR][1000 genomes]
rs940045	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9654010	0.84[EUR][1000 genomes]
rs974495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];1.00[ASN][1000 genomes]
rs9757181	1.00[CEU][hapmap]
rs9809237	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9817807	0.80[EUR][1000 genomes]
rs9824435	1.00[CHD][hapmap]
rs9835157	0.82[ASW][hapmap];1.00[CHD][hapmap];0.88[LWK][hapmap];0.95[MKK][hapmap];0.95[YRI][hapmap]
rs9842132	0.80[EUR][1000 genomes]
rs9849038	1.00[CHD][hapmap]
rs9860055	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9861027	0.82[EUR][1000 genomes]
rs9862534	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9870858	1.00[CHD][hapmap]
rs9871024	1.00[ASW][hapmap];1.00[CEU][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];0.95[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9883000	0.82[ASW][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap];0.95[MKK][hapmap];0.95[YRI][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:38)

SNP	Gene	Cis/trans	Tissue	Source
rs4241407	GNL3	cis	cerebellum	SCAN
rs4241407	AMT	cis	Esophagus Muscularis	GTEx
rs4241407	AMT	cis	Skin Sun Exposed Lower leg	GTEx
rs4241407	AMT	cis	Esophagus Mucosa	GTEx
rs4241407	WDR6	cis	parietal	SCAN
rs4241407	AMT	cis	Artery Aorta	GTEx
rs4241407	NICN1	cis	multi-tissue	Pritchard
rs4241407	P4HTM	cis	parietal	SCAN
rs4241407	WDR6	cis	Muscle Skeletal	GTEx
rs4241407	WDR6	cis	Nerve Tibial	GTEx
rs4241407	WDR6	cis	multi-tissue	Pritchard
rs4241407	DALRD3	cis	parietal	SCAN
rs4241407	NCKIPSD	cis	multi-tissue	Pritchard
rs4241407	AMT	cis	lymphoblastoid	seeQTL
rs4241407	NME6	cis	cerebellum	SCAN
rs4241407	AMT	cis	Thyroid	GTEx
rs4241407	NICN1	cis	cerebellum	SCAN
rs4241407	GPX1	cis	parietal	SCAN
rs4241407	AMT	cis	cerebellum	SCAN
rs4241407	AMT	cis	Muscle Skeletal	GTEx
rs4241407	SEMA3G	cis	cerebellum	SCAN
rs4241407	AMT	cis	Whole Blood	GTEx
rs4241407	AMT	cis	parietal	SCAN
rs4241407	NICN1	cis	Thyroid	GTEx
rs4241407	AMT	Cis_1M	lymphoblastoid	RTeQTL
rs4241407	AMT	cis	lung	GTEx
rs4241407	AMT	cis	Adipose Subcutaneous	GTEx
rs4241407	LZTFL1	cis	cerebellum	SCAN
rs4241407	AMT	cis	Artery Tibial	GTEx
rs4241407	DALRD3	cis	cerebellum	SCAN
rs4241407	AMT	cis	multi-tissue	Pritchard
rs4241407	WDR6	cis	cerebellum	SCAN
rs4241407	AMT	cis	Nerve Tibial	GTEx
rs4241407	GMPPB	cis	parietal	SCAN
rs4241407	ZNF589	cis	parietal	SCAN
rs4241407	WDR6	cis	Esophagus Muscularis	GTEx
rs4241407	NICN1-AS1	cis	Thyroid	GTEx
rs4241407	QRICH1	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49596000-49615000	Weak transcription	Brain Germinal Matrix	brain
2	chr3:49596000-49616800	Weak transcription	Fetal Brain Female	brain
3	chr3:49596200-49600400	Weak transcription	Brain Hippocampus Middle	brain
4	chr3:49597800-49600400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr3:49598000-49602000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:49598200-49601600	Weak transcription	Brain Angular Gyrus	brain
7	chr3:49598800-49603000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr3:49600000-49601000	Enhancers	Brain Anterior Caudate	brain
9	chr3:49600000-49601200	Enhancers	Brain Cingulate Gyrus	brain
10	chr3:49600000-49604800	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr3:49600000-49607800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr3:49600200-49600400	Enhancers	Brain Inferior Temporal Lobe	brain

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