Variant report

Variant	rs13098388
Chromosome Location	chr3:19995799-19995800
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11128927	0.96[ASN][1000 genomes]
rs11128928	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11128929	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11128930	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11128931	0.89[AFR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1143451	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12629485	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12631435	0.82[EUR][1000 genomes]
rs13065319	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13068289	0.81[EUR][1000 genomes]
rs13070718	0.83[EUR][1000 genomes]
rs13072891	0.86[ASN][1000 genomes]
rs13076973	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13077307	0.89[ASN][1000 genomes]
rs13078505	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13082980	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13086159	0.86[AFR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13089853	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13093485	0.81[EUR][1000 genomes]
rs13097697	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17181400	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17181862	0.93[AFR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17796115	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34305656	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34343204	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34417128	0.87[AFR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34705953	0.92[AFR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34872212	0.81[EUR][1000 genomes]
rs35175665	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35482904	0.83[ASN][1000 genomes]
rs35684714	0.81[EUR][1000 genomes]
rs35713165	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4610240	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58859849	0.87[ASN][1000 genomes]
rs59086970	0.91[ASN][1000 genomes]
rs59608170	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60255931	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6796425	0.85[AFR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71316239	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7434271	0.97[EUR][1000 genomes]
rs7614695	0.86[ASN][1000 genomes]
rs7615145	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7618928	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7633940	0.86[ASN][1000 genomes]
rs7634934	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7646128	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9877801	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9878879	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv433358	chr3:19547184-19996508	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs13098388	EFHB	cis	Thyroid	GTEx
rs13098388	EFHB	cis	Skin Sun Exposed Lower leg	GTEx
rs13098388	EFHB	cis	Artery Tibial	GTEx
rs13098388	EFHB	cis	Muscle Skeletal	GTEx
rs13098388	EFHB	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:126 , 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	chr3:19990800-19996600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
5	chr3:19990800-20017000	Weak transcription	Fetal Kidney	kidney
6	chr3:19991000-19996200	Weak transcription	Colon Smooth Muscle	Colon
7	chr3:19991000-19996600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr3:19991000-20001800	Weak transcription	Brain Angular Gyrus	brain
9	chr3:19991200-20002600	Weak transcription	Fetal Heart	heart
10	chr3:19991400-19998200	Weak transcription	Aorta	Aorta
11	chr3:19991400-19998800	Strong transcription	Fetal Thymus	thymus
12	chr3:19991400-20017000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr3:19991600-19997200	Strong transcription	NH-A	brain
14	chr3:19991600-19998400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr3:19991600-19998400	Weak transcription	Psoas Muscle	Psoas
16	chr3:19991600-20003800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:19991600-20003800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr3:19991800-19997600	Strong transcription	Primary B cells from peripheral blood	blood
19	chr3:19991800-19998000	Strong transcription	Fetal Intestine Large	intestine
20	chr3:19992000-19996200	Weak transcription	NHDF-Ad	bronchial
21	chr3:19992000-19998200	Strong transcription	K562	blood
22	chr3:19992000-20000000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr3:19992000-20000200	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr3:19992000-20000400	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr3:19992000-20003400	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr3:19992000-20004000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr3:19992200-19996600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr3:19992200-19998400	Strong transcription	Placenta	Placenta
29	chr3:19992200-20001000	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr3:19992200-20012200	Weak transcription	Stomach Mucosa	stomach
31	chr3:19992400-19997000	Strong transcription	H1 Cell Line	embryonic stem cell
32	chr3:19992400-19997400	Strong transcription	Sigmoid Colon	Sigmoid Colon
33	chr3:19992400-19997600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr3:19992400-19997600	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr3:19992400-19997800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr3:19992400-19997800	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr3:19992400-19998200	Strong transcription	Osteobl	bone
38	chr3:19992400-19998400	Strong transcription	Duodenum Mucosa	Duodenum
39	chr3:19992400-19998600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr3:19992400-19999000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr3:19992400-20001000	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr3:19992600-19998400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr3:19992600-20000400	Strong transcription	HSMM	muscle
44	chr3:19992600-20003800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr3:19992800-19998800	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr3:19992800-19999000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr3:19993000-19996200	Strong transcription	Adipose Nuclei	Adipose
48	chr3:19993000-19996400	Strong transcription	Brain Inferior Temporal Lobe	brain
49	chr3:19993000-19997800	Strong transcription	Brain Anterior Caudate	brain
50	chr3:19993000-19997800	Strong transcription	Rectal Mucosa Donor 31	rectum

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