Variant report

Variant	rs13070718
Chromosome Location	chr3:20003228-20003229
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:20001354..20003479-chr3:20064467..20066486,2	K562	blood:
2	chr3:19999505..20001254-chr3:20002139..20004557,2	MCF-7	breast:
3	chr3:20002287..20004974-chr3:20006037..20009711,3	K562	blood:
4	chr3:20002226..20004591-chr3:20006312..20009350,3	MCF-7	breast:
5	chr3:20002484..20004895-chr3:20024210..20026501,2	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11128928	0.82[CEU][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs11128929	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs11128930	0.82[CEU][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11128931	0.80[CEU][hapmap]
rs1143451	0.81[EUR][1000 genomes]
rs12629485	0.80[CEU][hapmap];0.80[EUR][1000 genomes]
rs13065319	0.87[TSI][hapmap]
rs13076973	0.83[EUR][1000 genomes]
rs13078505	0.81[AMR][1000 genomes]
rs13086159	0.80[EUR][1000 genomes]
rs13089853	0.83[EUR][1000 genomes]
rs13097409	1.00[ASW][hapmap]
rs13097697	0.81[EUR][1000 genomes]
rs13098388	0.83[EUR][1000 genomes]
rs17181400	0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs17181862	0.81[EUR][1000 genomes]
rs17678713	1.00[ASW][hapmap]
rs17796115	0.83[EUR][1000 genomes]
rs34305656	0.83[EUR][1000 genomes]
rs34343204	0.81[EUR][1000 genomes]
rs35175665	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35713165	0.83[EUR][1000 genomes]
rs4858768	1.00[ASW][hapmap]
rs59608170	0.85[EUR][1000 genomes]
rs6796425	0.80[EUR][1000 genomes]
rs71316239	0.81[EUR][1000 genomes]
rs7434271	0.81[EUR][1000 genomes]
rs7615145	0.83[EUR][1000 genomes]
rs7618928	0.82[EUR][1000 genomes]
rs7634934	0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs7646128	0.83[EUR][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13070718	EFHB	cis	Muscle Skeletal	GTEx
rs13070718	EFHB	cis	multi-tissue	Pritchard
rs13070718	EFHB	cis	cerebellum	SCAN
rs13070718	EFHB	cis	parietal	SCAN

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	chr3:19991400-20017000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr3:19991600-20003800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:19991600-20003800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr3:19992000-20003400	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr3:19992000-20004000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr3:19992200-20012200	Weak transcription	Stomach Mucosa	stomach
11	chr3:19992600-20003800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr3:19993600-20015600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr3:19993600-20023600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr3:19993800-20003600	Weak transcription	Primary hematopoietic stem cells	blood
15	chr3:19993800-20016200	Weak transcription	Rectal Smooth Muscle	rectum
16	chr3:19993800-20023800	Weak transcription	Small Intestine	intestine
17	chr3:19994000-20015800	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr3:19994000-20017400	Weak transcription	HSMMtube	muscle
19	chr3:19994600-20011600	Weak transcription	Brain Substantia Nigra	brain
20	chr3:19994600-20013800	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr3:19995600-20017000	Weak transcription	Brain Germinal Matrix	brain
22	chr3:19995800-20016800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr3:19995800-20021800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr3:19996400-20003400	Weak transcription	Left Ventricle	heart
25	chr3:19996400-20003800	Weak transcription	Esophagus	oesophagus
26	chr3:19996400-20017200	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr3:19996400-20021000	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr3:19996600-20003400	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr3:19996600-20007200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr3:19996600-20015600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr3:19996600-20016800	Weak transcription	Stomach Smooth Muscle	stomach
32	chr3:19996800-20007800	Weak transcription	Adipose Nuclei	Adipose
33	chr3:19997000-20003400	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr3:19997200-20013200	Weak transcription	HMEC	breast
35	chr3:19997200-20017000	Weak transcription	HUVEC	blood vessel
36	chr3:19997600-20011800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr3:19997600-20015200	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr3:19997800-20008400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr3:19997800-20013200	Weak transcription	NHLF	lung
40	chr3:19997800-20015400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr3:19997800-20015600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr3:19997800-20016200	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr3:19997800-20017000	Weak transcription	Brain Anterior Caudate	brain
44	chr3:19997800-20023200	Weak transcription	Spleen	Spleen
45	chr3:19998000-20003600	Weak transcription	Fetal Intestine Large	intestine
46	chr3:19998000-20011800	Weak transcription	Gastric	stomach
47	chr3:19998000-20017000	Weak transcription	HepG2	liver
48	chr3:19998200-20013200	Weak transcription	Osteobl	bone
49	chr3:19998400-20013200	Weak transcription	NHDF-Ad	bronchial
50	chr3:19998800-20003400	Weak transcription	Right Ventricle	heart

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