Variant report

Variant	rs13078505
Chromosome Location	chr3:20029447-20029448
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:20027598..20030041-chr3:20034679..20036338,2	K562	blood:
2	chr3:20027470..20029591-chr3:20033923..20036338,3	K562	blood:

Extended variants
information (count: 60 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs11128927	0.88[ASN][1000 genomes]
rs11128928	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11128929	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11128930	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11128931	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1143451	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12629485	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12631435	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13065319	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13068289	0.85[EUR][1000 genomes]
rs13070718	0.81[AMR][1000 genomes]
rs13072891	0.89[ASN][1000 genomes]
rs13076973	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13077307	0.82[ASN][1000 genomes]
rs13082980	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13086159	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13089853	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13093485	0.85[EUR][1000 genomes]
rs13097697	0.93[EUR][1000 genomes]
rs13098388	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17181400	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17181862	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17796115	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34305656	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34343204	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34417128	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34705953	0.85[ASN][1000 genomes]
rs34872212	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35175665	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35482904	0.85[ASN][1000 genomes]
rs35684714	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35713165	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4610240	0.93[EUR][1000 genomes]
rs59086970	0.84[ASN][1000 genomes]
rs59608170	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60255931	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6796425	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71316239	0.93[EUR][1000 genomes]
rs7434271	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7614695	0.89[ASN][1000 genomes]
rs7615145	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7618928	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7633940	0.89[ASN][1000 genomes]
rs7634934	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7643167	0.83[EUR][1000 genomes]
rs7646128	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9877801	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9878879	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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
11	nsv997486	chr3:20006702-20113989	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
12	esv1829542	chr3:20009231-20384627	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13078505	EFHB	cis	Artery Tibial	GTEx
rs13078505	EFHB	cis	Skin Sun Exposed Lower leg	GTEx
rs13078505	EFHB	cis	Muscle Skeletal	GTEx

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:20008800-20035600	Weak transcription	Psoas Muscle	Psoas
2	chr3:20012400-20033600	Weak transcription	Fetal Brain Male	brain
3	chr3:20015200-20030000	Strong transcription	Fetal Thymus	thymus
4	chr3:20023000-20045800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr3:20024000-20031200	Weak transcription	HSMM	muscle
6	chr3:20024000-20041400	Weak transcription	Ovary	ovary
7	chr3:20024200-20030600	Weak transcription	Hela-S3	cervix
8	chr3:20024200-20031000	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr3:20024200-20031200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr3:20024200-20031800	Weak transcription	Left Ventricle	heart
11	chr3:20024200-20033200	Weak transcription	Brain Cingulate Gyrus	brain
12	chr3:20024200-20033400	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr3:20024200-20036800	Weak transcription	Aorta	Aorta
14	chr3:20024200-20051400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr3:20024400-20029800	Weak transcription	Spleen	Spleen
16	chr3:20024400-20030600	Weak transcription	Thymus	Thymus
17	chr3:20024400-20034000	Weak transcription	Brain Germinal Matrix	brain
18	chr3:20024800-20030800	Weak transcription	Fetal Stomach	stomach
19	chr3:20024800-20031600	Weak transcription	Lung	lung
20	chr3:20024800-20031800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr3:20025400-20029600	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr3:20025400-20030600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr3:20025400-20031800	Weak transcription	Fetal Brain Female	brain
24	chr3:20025400-20033200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr3:20025600-20033400	Weak transcription	Brain Angular Gyrus	brain
26	chr3:20025800-20029800	Weak transcription	Brain Anterior Caudate	brain
27	chr3:20025800-20030400	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr3:20025800-20030600	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr3:20026200-20031000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr3:20026400-20030600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr3:20026400-20040800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr3:20026600-20031200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr3:20026800-20031800	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr3:20027000-20031800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr3:20027200-20030600	Weak transcription	Duodenum Mucosa	Duodenum
36	chr3:20027200-20031200	Weak transcription	Dnd41	blood
37	chr3:20027200-20033000	Weak transcription	Fetal Intestine Large	intestine
38	chr3:20027400-20029600	Weak transcription	Fetal Kidney	kidney
39	chr3:20027400-20029600	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr3:20027400-20036200	Weak transcription	NH-A	brain
41	chr3:20027600-20029600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr3:20027600-20030600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:20027600-20030600	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr3:20027600-20030600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr3:20027600-20031200	Weak transcription	Primary B cells from cord blood	blood
46	chr3:20027600-20032000	Weak transcription	Primary T cells from cord blood	blood
47	chr3:20027600-20033400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr3:20027600-20033400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr3:20027600-20036000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr3:20027800-20029600	Weak transcription	Primary B cells from peripheral blood	blood

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