Variant report

Variant	rs6774202
Chromosome Location	chr3:49687779-49687780
allele	G/T
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	chr3:49686939..49689819-chr3:49694987..49697482,3	K562	blood:
3	chr3:49687205..49689854-chr3:49709727..49711348,2	MCF-7	breast:

Extended variants
information (count: 70 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1009051	1.00[CHB][hapmap]
rs10452032	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1078341	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]
rs10865956	1.00[CHD][hapmap];0.84[LWK][hapmap];0.94[MKK][hapmap]
rs11130208	0.83[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];0.80[AMR][1000 genomes]
rs11130211	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11130217	0.92[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap]
rs11709734	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs11720705	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs11721148	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11928090	1.00[CHB][hapmap]
rs12583	1.00[CHD][hapmap];0.84[LWK][hapmap];0.94[MKK][hapmap]
rs12637313	0.88[CEU][hapmap];1.00[CHD][hapmap];0.83[TSI][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12715437	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap]
rs13096480	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13322887	1.00[CHD][hapmap];0.84[LWK][hapmap];0.94[MKK][hapmap]
rs1352889	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];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1463728	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1491983	0.92[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.83[TSI][hapmap];0.96[YRI][hapmap];0.84[AMR][1000 genomes]
rs1491985	1.00[CEU][hapmap]
rs1532204	0.94[CEU][hapmap];0.80[AMR][1000 genomes]
rs1586827	1.00[CEU][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1982861	1.00[CHD][hapmap];0.81[LWK][hapmap];0.94[MKK][hapmap]
rs1996663	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap]
rs1996664	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap]
rs2029591	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]
rs2131108	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2312462	1.00[CHD][hapmap];0.84[LWK][hapmap];0.94[MKK][hapmap]
rs2329021	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3020779	1.00[CEU][hapmap]
rs34890793	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap]
rs3866330	1.00[CHB][hapmap];0.80[LWK][hapmap];0.94[MKK][hapmap]
rs3905330	1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[LWK][hapmap];0.94[MKK][hapmap]
rs4241405	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]
rs4241407	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[LWK][hapmap];0.90[MKK][hapmap]
rs4855833	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];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4855845	1.00[CEU][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4855846	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4855848	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4855849	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][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];0.97[EUR][1000 genomes]
rs62262672	0.98[EUR][1000 genomes]
rs62262673	0.95[EUR][1000 genomes]
rs62262675	0.96[EUR][1000 genomes]
rs6446284	0.80[AMR][1000 genomes]
rs6446285	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap]
rs6446286	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6797299	0.94[CEU][hapmap];0.80[AMR][1000 genomes]
rs6809879	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap]
rs7613603	1.00[CEU][hapmap]
rs7620848	1.00[CEU][hapmap];0.83[YRI][hapmap]
rs7628207	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap]
rs7637711	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap]
rs7644148	1.00[CHD][hapmap];0.84[LWK][hapmap];0.94[MKK][hapmap]
rs7653505	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[MKK][hapmap]
rs9824435	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9829155	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap]
rs9830730	1.00[CEU][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9835157	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap]
rs9849038	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs9860055	1.00[CHD][hapmap];0.84[LWK][hapmap];0.90[MKK][hapmap]
rs9862534	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[LWK][hapmap];0.94[MKK][hapmap]
rs9870755	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap]
rs9870858	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs9871024	1.00[CHD][hapmap];0.84[LWK][hapmap];0.94[MKK][hapmap]
rs9883000	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	esv1796352	chr3:49687101-49949959	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs6774202	RNF123	cis	Artery Tibial	GTEx
rs6774202	GNL3	cis	cerebellum	SCAN
rs6774202	GMPPB	cis	parietal	SCAN
rs6774202	AMT	cis	parietal	SCAN
rs6774202	ZNF589	cis	parietal	SCAN
rs6774202	DALRD3	cis	cerebellum	SCAN
rs6774202	OR9G4	trans	parietal	SCAN
rs6774202	P4HTM	cis	parietal	SCAN
rs6774202	RNF123	cis	parietal	SCAN
rs6774202	AMT	cis	lung	GTEx
rs6774202	DALRD3	cis	parietal	SCAN
rs6774202	AMT	cis	Thyroid	GTEx

Chromatin state (count:46 , 50 per page) page: 1

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	chr3:49676200-49692000	Weak transcription	Esophagus	oesophagus
6	chr3:49681200-49688600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:49681200-49688800	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr3:49682200-49689000	Weak transcription	Brain Cingulate Gyrus	brain
9	chr3:49682600-49688400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr3:49684600-49687800	Genic enhancers	Brain Inferior Temporal Lobe	brain
11	chr3:49684800-49688000	Enhancers	HepG2	liver
12	chr3:49684800-49688400	Enhancers	Fetal Muscle Leg	muscle
13	chr3:49684800-49688800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr3:49684800-49689400	Enhancers	Fetal Muscle Trunk	muscle
15	chr3:49685200-49708200	Strong transcription	Brain Germinal Matrix	brain
16	chr3:49685400-49690400	Weak transcription	Lung	lung
17	chr3:49685400-49708400	Strong transcription	Fetal Brain Female	brain
18	chr3:49685600-49693200	Weak transcription	Liver	Liver
19	chr3:49685800-49688400	Weak transcription	Brain Hippocampus Middle	brain
20	chr3:49685800-49688400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr3:49685800-49689000	Weak transcription	Fetal Stomach	stomach
22	chr3:49685800-49689600	Weak transcription	Brain Substantia Nigra	brain
23	chr3:49685800-49692600	Weak transcription	Fetal Intestine Small	intestine
24	chr3:49686000-49688400	Weak transcription	Brain Anterior Caudate	brain
25	chr3:49686000-49689000	Weak transcription	Brain Angular Gyrus	brain
26	chr3:49686000-49692400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr3:49686000-49692600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr3:49686400-49687800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr3:49686600-49688200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr3:49686600-49697200	Weak transcription	Pancreas	Pancrea
31	chr3:49686600-49710600	Weak transcription	Right Atrium	heart
32	chr3:49686800-49687800	Enhancers	Primary hematopoietic stem cells	blood
33	chr3:49687000-49687800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr3:49687000-49687800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr3:49687000-49687800	Enhancers	Fetal Thymus	thymus
36	chr3:49687000-49688600	Enhancers	GM12878-XiMat	blood
37	chr3:49687000-49695600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr3:49687400-49687800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr3:49687600-49687800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:49687600-49687800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr3:49687600-49689000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr3:49687600-49689000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr3:49687600-49691600	Weak transcription	Spleen	Spleen
44	chr3:49687600-49694200	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr3:49687600-49702400	Weak transcription	Right Ventricle	heart
46	chr3:49687600-49705800	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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