Variant report

Variant	rs4241405
Chromosome Location	chr3:49642027-49642028
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 100 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs10452032	0.91[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1078341	0.91[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10865956	0.91[ASW][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap];0.98[MKK][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11130190	1.00[ASN][1000 genomes]
rs11130204	0.82[AFR][1000 genomes]
rs11130207	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130208	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130211	1.00[CEU][hapmap];0.85[YRI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11130217	0.91[ASW][hapmap];0.89[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs11709734	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs11720657	1.00[ASN][1000 genomes]
rs11720705	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs11721148	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12583	0.91[ASW][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap];0.98[MKK][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12637313	0.83[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12715437	0.91[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs13096474	1.00[CHD][hapmap];0.89[MKK][hapmap]
rs13096480	1.00[YRI][hapmap];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13322887	0.91[ASW][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap];0.98[MKK][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1352889	0.83[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.83[TSI][hapmap];0.87[YRI][hapmap];0.89[AMR][1000 genomes]
rs1463728	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1491983	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1491985	0.94[CEU][hapmap];0.83[YRI][hapmap];1.00[ASN][1000 genomes]
rs1532204	1.00[CEU][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1586827	0.94[CEU][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1982861	0.91[ASW][hapmap];1.00[CHD][hapmap];0.91[LWK][hapmap];0.98[MKK][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes]
rs2029591	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];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2131108	0.91[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2140270	1.00[ASN][1000 genomes]
rs2177268	1.00[ASN][1000 genomes]
rs2312462	0.91[ASW][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap];0.98[MKK][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes]
rs2329021	0.91[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3020779	0.93[CEU][hapmap];0.91[YRI][hapmap];1.00[ASN][1000 genomes]
rs3448	1.00[ASN][1000 genomes]
rs34890793	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap]
rs3866330	0.92[MKK][hapmap]
rs3905330	1.00[CHD][hapmap];0.92[MKK][hapmap]
rs4052546	0.86[AFR][1000 genomes]
rs4241407	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	0.83[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.83[TSI][hapmap];0.87[YRI][hapmap];0.89[AMR][1000 genomes]
rs4855837	0.86[AFR][1000 genomes]
rs4855845	0.94[CEU][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4855846	0.91[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4855848	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4855849	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4855853	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4855882	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[TSI][hapmap]
rs4855885	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs4955430	1.00[ASN][1000 genomes]
rs56127630	1.00[ASN][1000 genomes]
rs62259933	1.00[ASN][1000 genomes]
rs62259943	1.00[ASN][1000 genomes]
rs62259944	1.00[ASN][1000 genomes]
rs62259947	1.00[ASN][1000 genomes]
rs62261249	1.00[ASN][1000 genomes]
rs62262672	1.00[ASN][1000 genomes]
rs62262673	1.00[ASN][1000 genomes]
rs62262675	1.00[ASN][1000 genomes]
rs6446275	1.00[ASN][1000 genomes]
rs6446284	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6446285	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446286	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6774202	0.83[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.83[TSI][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes]
rs6785045	1.00[ASN][1000 genomes]
rs6797299	1.00[CEU][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6805609	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs6809204	1.00[ASN][1000 genomes]
rs6809879	0.81[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap]
rs72934271	1.00[ASN][1000 genomes]
rs73088137	1.00[ASN][1000 genomes]
rs7355800	1.00[ASN][1000 genomes]
rs7613491	1.00[ASN][1000 genomes]
rs7613603	0.94[CEU][hapmap]
rs7620848	0.92[CEU][hapmap];1.00[YRI][hapmap]
rs7628207	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap]
rs7637711	0.91[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap]
rs7638750	1.00[ASN][1000 genomes]
rs7644148	0.91[ASW][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap];0.98[MKK][hapmap];0.91[YRI][hapmap]
rs7647973	1.00[ASN][1000 genomes]
rs7648995	1.00[ASN][1000 genomes]
rs7651372	1.00[ASN][1000 genomes]
rs7653505	1.00[CHD][hapmap];0.86[MKK][hapmap]
rs8897	0.91[ASW][hapmap];1.00[CHD][hapmap];0.83[LWK][hapmap];0.80[MKK][hapmap];0.91[YRI][hapmap];1.00[ASN][1000 genomes]
rs940045	1.00[CHD][hapmap];0.89[MKK][hapmap]
rs9817807	1.00[ASN][1000 genomes]
rs9824435	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs9829155	0.91[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap]
rs9830730	0.94[CEU][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9835157	0.91[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap]
rs9842132	1.00[ASN][1000 genomes]
rs9849038	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs9860055	0.91[ASW][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap];0.95[MKK][hapmap];0.91[YRI][hapmap];1.00[ASN][1000 genomes]
rs9861027	1.00[ASN][1000 genomes]
rs9862534	1.00[CHD][hapmap];0.92[MKK][hapmap]
rs9870755	0.91[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap]
rs9870858	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs9871024	0.91[ASW][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap];0.98[MKK][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9883000	0.91[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];1.00[ASN][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	nsv508217	chr3:49615446-49769896	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	esv3324697	chr3:49641773-49644321	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs4241405	LZTFL1	cis	cerebellum	SCAN
rs4241405	DALRD3	cis	parietal	SCAN
rs4241405	WDR6	cis	cerebellum	SCAN
rs4241405	AMT	cis	parietal	SCAN
rs4241405	NICN1	cis	Thyroid	GTEx
rs4241405	GMPPB	cis	parietal	SCAN
rs4241405	AMT	cis	cerebellum	SCAN
rs4241405	AMT	cis	Thyroid	GTEx
rs4241405	ZNF589	cis	parietal	SCAN
rs4241405	GNL3	cis	cerebellum	SCAN
rs4241405	QRICH1	cis	cerebellum	SCAN
rs4241405	RNF123	cis	parietal	SCAN
rs4241405	AMT	cis	Nerve Tibial	GTEx
rs4241405	NME6	cis	cerebellum	SCAN
rs4241405	P4HTM	cis	parietal	SCAN
rs4241405	AMT	cis	lymphoblastoid	seeQTL
rs4241405	DALRD3	cis	cerebellum	SCAN
rs4241405	ARIH2	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49637800-49653600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:49638000-49644600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:49638000-49647200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr3:49639200-49643800	Weak transcription	Brain Anterior Caudate	brain
5	chr3:49639800-49644000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr3:49639800-49644000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr3:49639800-49644600	Weak transcription	NHDF-Ad	bronchial
8	chr3:49640400-49646800	Weak transcription	Brain Cingulate Gyrus	brain
9	chr3:49640600-49644000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr3:49640600-49644200	Weak transcription	Hela-S3	cervix
11	chr3:49640600-49644800	Weak transcription	Brain Angular Gyrus	brain
12	chr3:49640600-49647000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr3:49640800-49646800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr3:49641000-49643800	Weak transcription	Spleen	Spleen
15	chr3:49641000-49644000	Weak transcription	Pancreas	Pancrea
16	chr3:49641000-49644600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:49641200-49644400	Weak transcription	HMEC	breast
18	chr3:49641200-49644400	Weak transcription	NHEK	skin
19	chr3:49641200-49644600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr3:49641200-49653600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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