Variant report

Variant	rs1078341
Chromosome Location	chr3:49685592-49685593
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:49576104..49578514-chr3:49684857..49687792,2	MCF-7	breast:
2	chr3:49683730..49686310-chr3:49694623..49697344,2	K562	blood:
3	chr3:49676360..49678118-chr3:49683625..49686002,2	K562	blood:

Extended variants
information (count: 95 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10452032	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[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]
rs10865956	0.82[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	1.00[ASN][1000 genomes]
rs11130208	0.91[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[YRI][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11130211	0.94[CEU][hapmap];0.84[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11130217	1.00[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];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs11709734	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs11720705	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs11721148	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12583	0.82[ASW][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap];0.98[MKK][hapmap];0.95[YRI][hapmap];1.00[ASN][1000 genomes]
rs12637313	0.88[CEU][hapmap];1.00[CHD][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]
rs12715437	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs13096480	1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13322887	0.82[ASW][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap];0.98[MKK][hapmap];0.95[YRI][hapmap];1.00[ASN][1000 genomes]
rs1352889	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1463728	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1491983	0.82[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.83[TSI][hapmap];0.87[YRI][hapmap];0.84[AMR][1000 genomes]
rs1491985	1.00[CEU][hapmap];0.83[YRI][hapmap];1.00[ASN][1000 genomes]
rs1532204	0.94[CEU][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1586827	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1982861	0.82[ASW][hapmap];1.00[CHD][hapmap];0.91[LWK][hapmap];0.98[MKK][hapmap];0.95[YRI][hapmap]
rs1996663	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap]
rs1996664	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap]
rs2029591	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]
rs2131108	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];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2140270	1.00[ASN][1000 genomes]
rs2177268	1.00[ASN][1000 genomes]
rs2312462	0.82[ASW][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap];0.98[MKK][hapmap];0.95[YRI][hapmap]
rs2329021	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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3020779	1.00[CEU][hapmap];0.91[YRI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34890793	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap]
rs3866330	0.92[MKK][hapmap]
rs3905330	1.00[CHD][hapmap];0.92[MKK][hapmap]
rs4241405	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]
rs4241407	0.82[ASW][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap];0.95[MKK][hapmap];0.95[YRI][hapmap]
rs4855833	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4855845	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855846	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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855848	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855849	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855853	1.00[ASN][1000 genomes]
rs4855882	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs4855885	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55754265	0.81[EUR][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]
rs62262671	0.81[EUR][1000 genomes]
rs62262672	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262673	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262675	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446275	1.00[ASN][1000 genomes]
rs6446284	0.80[AMR][1000 genomes]
rs6446285	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[ASN][1000 genomes]
rs6446286	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6774202	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[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]
rs6785045	1.00[ASN][1000 genomes]
rs6797299	0.94[CEU][hapmap];0.94[YRI][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6805609	1.00[ASN][1000 genomes]
rs6809879	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[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	1.00[CEU][hapmap]
rs7620848	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs7628207	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap]
rs7637711	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs7638750	1.00[ASN][1000 genomes]
rs7644148	0.82[ASW][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap];0.98[MKK][hapmap];0.95[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];0.85[MKK][hapmap]
rs8897	1.00[ASN][1000 genomes]
rs9817807	1.00[ASN][1000 genomes]
rs9824435	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9829155	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs9830730	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9835157	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs9842132	1.00[ASN][1000 genomes]
rs9849038	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs9860055	0.82[ASW][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap];0.95[MKK][hapmap];0.95[YRI][hapmap];1.00[ASN][1000 genomes]
rs9861027	1.00[ASN][1000 genomes]
rs9862534	1.00[CHD][hapmap];0.92[MKK][hapmap]
rs9870755	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs9870858	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs9871024	0.82[ASW][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap];0.98[MKK][hapmap];0.95[YRI][hapmap];1.00[ASN][1000 genomes]
rs9883000	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];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][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	nsv1011428	chr3:49649989-49706068	Enhancers Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs1078341	OR9G4	trans	parietal	SCAN
rs1078341	ZNF589	cis	parietal	SCAN
rs1078341	AMT	cis	Thyroid	GTEx
rs1078341	RNF123	cis	parietal	SCAN
rs1078341	P4HTM	cis	parietal	SCAN
rs1078341	DALRD3	cis	cerebellum	SCAN
rs1078341	DALRD3	cis	parietal	SCAN
rs1078341	NICN1	cis	multi-tissue	Pritchard
rs1078341	AMT	cis	parietal	SCAN
rs1078341	RNF123	cis	Artery Tibial	GTEx
rs1078341	GNL3	cis	cerebellum	SCAN
rs1078341	GMPPB	cis	parietal	SCAN
rs1078341	QRICH1	cis	cerebellum	SCAN
rs1078341	AMT	cis	lung	GTEx

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49661600-49692400	Weak transcription	Ovary	ovary
2	chr3:49669400-49692000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr3:49673800-49692400	Weak transcription	Gastric	stomach
4	chr3:49675400-49688200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr3:49676000-49686400	Weak transcription	Spleen	Spleen
6	chr3:49676200-49692000	Weak transcription	Esophagus	oesophagus
7	chr3:49676400-49687000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr3:49679600-49687000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr3:49679800-49687600	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr3:49681200-49688600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:49681200-49688800	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr3:49682200-49689000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr3:49682600-49688400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr3:49683000-49687000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr3:49683200-49686000	Enhancers	Brain Angular Gyrus	brain
16	chr3:49683200-49686600	Enhancers	Pancreas	Pancrea
17	chr3:49684400-49685800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr3:49684600-49685600	Enhancers	Primary hematopoietic stem cells	blood
19	chr3:49684600-49686000	Enhancers	Adipose Nuclei	Adipose
20	chr3:49684600-49686000	Enhancers	Brain Anterior Caudate	brain
21	chr3:49684600-49686600	Enhancers	Right Atrium	heart
22	chr3:49684600-49687400	Enhancers	Fetal Heart	heart
23	chr3:49684600-49687800	Genic enhancers	Brain Inferior Temporal Lobe	brain
24	chr3:49684800-49685800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
25	chr3:49684800-49686000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr3:49684800-49687400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr3:49684800-49687400	Enhancers	Left Ventricle	heart
28	chr3:49684800-49687600	Enhancers	Psoas Muscle	Psoas
29	chr3:49684800-49688000	Enhancers	HepG2	liver
30	chr3:49684800-49688400	Enhancers	Fetal Muscle Leg	muscle
31	chr3:49684800-49688800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr3:49684800-49689400	Enhancers	Fetal Muscle Trunk	muscle
33	chr3:49685000-49685600	Enhancers	Liver	Liver
34	chr3:49685000-49686000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr3:49685000-49686000	Enhancers	Hela-S3	cervix
36	chr3:49685000-49686200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr3:49685000-49686200	Enhancers	Fetal Lung	lung
38	chr3:49685000-49686600	Enhancers	Right Ventricle	heart
39	chr3:49685000-49687400	Enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr3:49685000-49687600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:49685200-49685600	Enhancers	NH-A	brain
42	chr3:49685200-49685800	Enhancers	Brain Hippocampus Middle	brain
43	chr3:49685200-49686000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr3:49685200-49686000	Enhancers	GM12878-XiMat	blood
45	chr3:49685200-49708200	Strong transcription	Brain Germinal Matrix	brain
46	chr3:49685400-49685600	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr3:49685400-49685800	Enhancers	Brain Substantia Nigra	brain
48	chr3:49685400-49685800	Enhancers	Fetal Stomach	stomach
49	chr3:49685400-49686000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
50	chr3:49685400-49687600	Enhancers	K562	blood

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