Variant report

Variant	rs2029591
Chromosome Location	chr3:49646981-49646982
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 95 )
Associated
traits (count: 21 )

rSNPs within LD-proxies of this variant (count:94)

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];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][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];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][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];1.00[ASN][1000 genomes]
rs11130190	1.00[ASN][1000 genomes]
rs11130207	0.84[AMR][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];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130211	1.00[CEU][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12583	0.91[ASW][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap];0.98[MKK][hapmap];0.95[YRI][hapmap];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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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]
rs13096480	1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][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];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];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1463728	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1491985	0.94[CEU][hapmap];0.83[YRI][hapmap];1.00[ASN][1000 genomes]
rs1532204	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1586827	0.94[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][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]
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];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][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]
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];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][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]
rs4241405	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]
rs4241407	0.91[ASW][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap];0.95[MKK][hapmap];0.95[YRI][hapmap]
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];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4855845	0.94[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][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];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855848	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855849	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855853	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];0.86[EUR][1000 genomes];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	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262673	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262675	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446275	1.00[ASN][1000 genomes]
rs6446284	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6446285	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446286	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][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];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6785045	1.00[ASN][1000 genomes]
rs6797299	1.00[CEU][hapmap];0.94[YRI][hapmap];0.86[AMR][1000 genomes];0.81[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];0.87[EUR][1000 genomes];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];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][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];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];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][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	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

mRNA abundance (count:21)

SNP	Gene	Cis/trans	Tissue	Source
rs2029591	WDR6	cis	multi-tissue	Pritchard
rs2029591	GNL3	cis	cerebellum	SCAN
rs2029591	AMT	cis	Thyroid	GTEx
rs2029591	GMPPB	cis	parietal	SCAN
rs2029591	P4HTM	cis	parietal	SCAN
rs2029591	NICN1	cis	Thyroid	GTEx
rs2029591	AMT	cis	Nerve Tibial	GTEx
rs2029591	WDR6	cis	cerebellum	SCAN
rs2029591	ARIH2	cis	cerebellum	SCAN
rs2029591	RNF123	cis	parietal	SCAN
rs2029591	ZNF589	cis	parietal	SCAN
rs2029591	AMT	cis	multi-tissue	Pritchard
rs2029591	DALRD3	cis	parietal	SCAN
rs2029591	AMT	cis	cerebellum	SCAN
rs2029591	DALRD3	cis	cerebellum	SCAN
rs2029591	NICN1	cis	multi-tissue	Pritchard
rs2029591	AMT	cis	lymphoblastoid	seeQTL
rs2029591	AMT	cis	parietal	SCAN
rs2029591	NME6	cis	cerebellum	SCAN
rs2029591	QRICH1	cis	cerebellum	SCAN
rs2029591	LZTFL1	cis	cerebellum	SCAN

Chromatin state (count:30 , 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	chr3:49638000-49647200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr3:49640600-49647000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:49641200-49653600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:49644600-49648800	Weak transcription	Fetal Muscle Trunk	muscle
6	chr3:49645000-49647200	Weak transcription	Left Ventricle	heart
7	chr3:49645200-49647000	Weak transcription	Fetal Brain Male	brain
8	chr3:49645400-49647000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr3:49645400-49647200	Weak transcription	Brain Germinal Matrix	brain
10	chr3:49645400-49648200	Weak transcription	Esophagus	oesophagus
11	chr3:49645400-49648200	Weak transcription	Stomach Mucosa	stomach
12	chr3:49645800-49647400	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr3:49645800-49653600	Weak transcription	Fetal Lung	lung
14	chr3:49646600-49649200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
15	chr3:49646800-49647000	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr3:49646800-49647200	Enhancers	Pancreatic Islets	Pancreatic Islet
17	chr3:49646800-49647200	Enhancers	Right Ventricle	heart
18	chr3:49646800-49647400	Enhancers	Fetal Brain Female	brain
19	chr3:49646800-49647600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr3:49646800-49647600	Enhancers	Stomach Smooth Muscle	stomach
21	chr3:49646800-49647800	Enhancers	Fetal Heart	heart
22	chr3:49646800-49648400	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr3:49646800-49648600	Enhancers	Brain Hippocampus Middle	brain
24	chr3:49646800-49648600	Enhancers	Brain Inferior Temporal Lobe	brain
25	chr3:49646800-49648600	Enhancers	Brain Substantia Nigra	brain
26	chr3:49646800-49648600	Enhancers	Fetal Stomach	stomach
27	chr3:49646800-49648800	Enhancers	Brain Angular Gyrus	brain
28	chr3:49646800-49649000	Enhancers	Brain Anterior Caudate	brain
29	chr3:49646800-49649000	Enhancers	Brain Cingulate Gyrus	brain
30	chr3:49646800-49649400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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