Variant report

Variant	rs6550239
Chromosome Location	chr3:20001318-20001319
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:20000869..20003143-chr3:20080337..20083927,3	K562	blood:
2	chr3:19998852..20001425-chr3:20020103..20022422,2	MCF-7	breast:
3	chr3:19988063..19990620-chr3:20000922..20003019,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114166	Chromatin interaction
ENSG00000144566	Chromatin interaction
ENSG00000163576	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11718997	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12714980	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13085450	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13085694	0.88[ASN][1000 genomes]
rs2127956	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2364515	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2929343	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2929415	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2948110	0.80[ASN][1000 genomes]
rs2948111	0.80[ASN][1000 genomes]
rs4858626	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4858652	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6550237	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6773437	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6797890	0.89[ASN][1000 genomes]
rs6803052	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7616422	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7627200	0.99[ASN][1000 genomes]
rs9840653	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9858341	0.92[ASN][1000 genomes]
rs9968079	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1828161	chr3:19547184-20062060	Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	esv1825914	chr3:19549859-20137270	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	esv1833006	chr3:19562271-20389045	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	esv1826570	chr3:19579860-20077414	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	esv1833139	chr3:19579860-20121349	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	esv1826254	chr3:19592688-20042834	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv1010613	chr3:19942032-20461486	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
8	esv1826030	chr3:19972766-20170581	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
9	esv1825988	chr3:19976375-20102773	Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
10	esv1826830	chr3:19982972-20632072	Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6550239	EFHB	cis	Artery Tibial	GTEx
rs6550239	EFHB	cis	Esophagus Muscularis	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:19989800-20018800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:19990000-20008600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:19990000-20016200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr3:19990800-20017000	Weak transcription	Fetal Kidney	kidney
5	chr3:19991000-20001800	Weak transcription	Brain Angular Gyrus	brain
6	chr3:19991200-20002600	Weak transcription	Fetal Heart	heart
7	chr3:19991400-20017000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr3:19991600-20003800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:19991600-20003800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr3:19992000-20003400	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr3:19992000-20004000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr3:19992200-20012200	Weak transcription	Stomach Mucosa	stomach
13	chr3:19992600-20003800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:19993600-20015600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr3:19993600-20023600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr3:19993800-20003600	Weak transcription	Primary hematopoietic stem cells	blood
17	chr3:19993800-20016200	Weak transcription	Rectal Smooth Muscle	rectum
18	chr3:19993800-20023800	Weak transcription	Small Intestine	intestine
19	chr3:19994000-20015800	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr3:19994000-20017400	Weak transcription	HSMMtube	muscle
21	chr3:19994600-20011600	Weak transcription	Brain Substantia Nigra	brain
22	chr3:19994600-20013800	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr3:19995000-20002400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr3:19995600-20017000	Weak transcription	Brain Germinal Matrix	brain
25	chr3:19995800-20016800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr3:19995800-20021800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr3:19996000-20002200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
28	chr3:19996400-20003200	Genic enhancers	Primary T helper cells PMA-I stimulated	--
29	chr3:19996400-20003400	Weak transcription	Left Ventricle	heart
30	chr3:19996400-20003800	Weak transcription	Esophagus	oesophagus
31	chr3:19996400-20017200	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr3:19996400-20021000	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr3:19996600-20002000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr3:19996600-20003400	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr3:19996600-20007200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr3:19996600-20015600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr3:19996600-20016800	Weak transcription	Stomach Smooth Muscle	stomach
38	chr3:19996800-20002800	Weak transcription	Fetal Brain Female	brain
39	chr3:19996800-20007800	Weak transcription	Adipose Nuclei	Adipose
40	chr3:19997000-20003400	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr3:19997200-20013200	Weak transcription	HMEC	breast
42	chr3:19997200-20017000	Weak transcription	HUVEC	blood vessel
43	chr3:19997600-20001400	Weak transcription	Primary B cells from peripheral blood	blood
44	chr3:19997600-20011800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr3:19997600-20015200	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr3:19997800-20002800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr3:19997800-20003000	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr3:19997800-20008400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chr3:19997800-20013200	Weak transcription	NHLF	lung
50	chr3:19997800-20015400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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