Variant report

Variant	rs4855845
Chromosome Location	chr3:49687043-49687044
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49576104..49578514-chr3:49684857..49687792,2	MCF-7	breast:
2	chr3:49686939..49689819-chr3:49694987..49697482,3	K562	blood:

Extended variants
information (count: 91 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10452032	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]
rs1078341	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]
rs10865956	0.95[YRI][hapmap];1.00[ASN][1000 genomes]
rs11130190	1.00[ASN][1000 genomes]
rs11130207	1.00[ASN][1000 genomes]
rs11130208	0.94[CEU][hapmap];0.95[YRI][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11130211	0.94[CEU][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11130217	0.94[CEU][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs11709734	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs11720705	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs11721148	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12583	0.95[YRI][hapmap];1.00[ASN][1000 genomes]
rs12637313	0.87[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]
rs12715437	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs13096480	1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13322887	0.90[YRI][hapmap];1.00[ASN][1000 genomes]
rs1352889	1.00[CEU][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1463728	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1491983	0.94[CEU][hapmap];0.91[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];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1982861	0.95[YRI][hapmap]
rs1996663	1.00[CEU][hapmap];0.90[YRI][hapmap]
rs1996664	1.00[CEU][hapmap];0.90[YRI][hapmap]
rs2029591	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]
rs2131108	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[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	0.95[YRI][hapmap]
rs2329021	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]
rs3020779	1.00[CEU][hapmap];0.91[YRI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34890793	0.94[CEU][hapmap]
rs4241405	0.94[CEU][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4241407	0.95[YRI][hapmap]
rs4855833	1.00[CEU][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4855846	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]
rs4855848	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855849	0.97[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]
rs4855885	1.00[CEU][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[ASN][1000 genomes]
rs6446286	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6774202	1.00[CEU][hapmap];0.87[YRI][hapmap];0.86[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	1.00[CEU][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]
rs7637711	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs7638750	1.00[ASN][1000 genomes]
rs7644148	0.90[YRI][hapmap]
rs7647973	1.00[ASN][1000 genomes]
rs7648995	1.00[ASN][1000 genomes]
rs7651372	1.00[ASN][1000 genomes]
rs8897	1.00[ASN][1000 genomes]
rs9817807	1.00[ASN][1000 genomes]
rs9824435	1.00[CEU][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9829155	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs9830730	1.00[CEU][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9835157	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs9842132	1.00[ASN][1000 genomes]
rs9849038	1.00[CEU][hapmap]
rs9860055	0.90[YRI][hapmap];1.00[ASN][1000 genomes]
rs9861027	1.00[ASN][1000 genomes]
rs9870755	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs9870858	1.00[CEU][hapmap]
rs9871024	0.90[YRI][hapmap];1.00[ASN][1000 genomes]
rs9883000	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4855845	RNF123	cis	Artery Tibial	GTEx
rs4855845	AMT	cis	Thyroid	GTEx
rs4855845	AMT	cis	lung	GTEx

Chromatin state (count:55 , 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	chr3:49676200-49692000	Weak transcription	Esophagus	oesophagus
6	chr3:49679800-49687600	Enhancers	Skeletal Muscle Female	skeletal muscle
7	chr3:49681200-49688600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:49681200-49688800	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr3:49682200-49689000	Weak transcription	Brain Cingulate Gyrus	brain
10	chr3:49682600-49688400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr3:49684600-49687400	Enhancers	Fetal Heart	heart
12	chr3:49684600-49687800	Genic enhancers	Brain Inferior Temporal Lobe	brain
13	chr3:49684800-49687400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr3:49684800-49687400	Enhancers	Left Ventricle	heart
15	chr3:49684800-49687600	Enhancers	Psoas Muscle	Psoas
16	chr3:49684800-49688000	Enhancers	HepG2	liver
17	chr3:49684800-49688400	Enhancers	Fetal Muscle Leg	muscle
18	chr3:49684800-49688800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr3:49684800-49689400	Enhancers	Fetal Muscle Trunk	muscle
20	chr3:49685000-49687400	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr3:49685000-49687600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr3:49685200-49708200	Strong transcription	Brain Germinal Matrix	brain
23	chr3:49685400-49687600	Enhancers	K562	blood
24	chr3:49685400-49690400	Weak transcription	Lung	lung
25	chr3:49685400-49708400	Strong transcription	Fetal Brain Female	brain
26	chr3:49685600-49693200	Weak transcription	Liver	Liver
27	chr3:49685800-49688400	Weak transcription	Brain Hippocampus Middle	brain
28	chr3:49685800-49688400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr3:49685800-49689000	Weak transcription	Fetal Stomach	stomach
30	chr3:49685800-49689600	Weak transcription	Brain Substantia Nigra	brain
31	chr3:49685800-49692600	Weak transcription	Fetal Intestine Small	intestine
32	chr3:49686000-49687600	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr3:49686000-49688400	Weak transcription	Brain Anterior Caudate	brain
34	chr3:49686000-49689000	Weak transcription	Brain Angular Gyrus	brain
35	chr3:49686000-49692400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr3:49686000-49692600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr3:49686400-49687600	Enhancers	Spleen	Spleen
38	chr3:49686400-49687800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr3:49686600-49688200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr3:49686600-49697200	Weak transcription	Pancreas	Pancrea
41	chr3:49686600-49710600	Weak transcription	Right Atrium	heart
42	chr3:49686800-49687800	Enhancers	Primary hematopoietic stem cells	blood
43	chr3:49687000-49687200	Enhancers	Placenta Amnion	Placenta Amnion
44	chr3:49687000-49687200	Enhancers	NH-A	brain
45	chr3:49687000-49687400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr3:49687000-49687400	Enhancers	NHEK	skin
47	chr3:49687000-49687600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr3:49687000-49687600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr3:49687000-49687600	Enhancers	Right Ventricle	heart
50	chr3:49687000-49687600	Enhancers	HMEC	breast

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