Variant report

Variant	rs6796425
Chromosome Location	chr3:20016593-20016594
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:19987383..19992426-chr3:20011245..20019650,13	MCF-7	breast:
2	chr3:19987782..19990680-chr3:20013275..20017779,4	K562	blood:
3	chr3:20007536..20010825-chr3:20014102..20016831,3	K562	blood:

Variant related genes	Relation type
ENSG00000144566	Chromatin interaction
ENSG00000163576	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs11128927	0.89[ASN][1000 genomes]
rs11128928	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11128929	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11128930	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11128931	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1143451	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12629485	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12631435	0.83[EUR][1000 genomes]
rs13065319	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13068289	0.82[EUR][1000 genomes]
rs13070718	0.80[EUR][1000 genomes]
rs13072891	0.90[ASN][1000 genomes]
rs13076973	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13077307	0.83[ASN][1000 genomes]
rs13078505	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13082980	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13086159	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13089853	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13093485	0.82[EUR][1000 genomes]
rs13097697	0.80[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs13098388	0.85[AFR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17181400	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17181862	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17796115	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34305656	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34343204	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34417128	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34705953	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs34872212	0.82[EUR][1000 genomes]
rs35175665	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35482904	0.86[ASN][1000 genomes]
rs35684714	0.82[EUR][1000 genomes]
rs35713165	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4610240	0.80[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs4858121	0.81[ASN][1000 genomes]
rs58859849	0.81[ASN][1000 genomes]
rs59086970	0.85[ASN][1000 genomes]
rs59608170	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60255931	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71316239	0.85[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs7434271	0.94[EUR][1000 genomes]
rs7614695	0.90[ASN][1000 genomes]
rs7615145	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7618928	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7633940	0.90[ASN][1000 genomes]
rs7634934	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7643167	0.80[EUR][1000 genomes]
rs7646128	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9877801	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9878879	0.91[EUR][1000 genomes];0.95[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6796425	EFHB	cis	Muscle Skeletal	GTEx
rs6796425	EFHB	cis	Skin Sun Exposed Lower leg	GTEx
rs6796425	EFHB	cis	Adipose Subcutaneous	GTEx
rs6796425	EFHB	cis	Thyroid	GTEx
rs6796425	EFHB	cis	Artery Tibial	GTEx

Chromatin state (count:124 , 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	chr3:19990800-20017000	Weak transcription	Fetal Kidney	kidney
3	chr3:19991400-20017000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr3:19993600-20023600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:19993800-20023800	Weak transcription	Small Intestine	intestine
6	chr3:19994000-20017400	Weak transcription	HSMMtube	muscle
7	chr3:19995600-20017000	Weak transcription	Brain Germinal Matrix	brain
8	chr3:19995800-20016800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr3:19995800-20021800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr3:19996400-20017200	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr3:19996400-20021000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr3:19996600-20016800	Weak transcription	Stomach Smooth Muscle	stomach
13	chr3:19997200-20017000	Weak transcription	HUVEC	blood vessel
14	chr3:19997800-20017000	Weak transcription	Brain Anterior Caudate	brain
15	chr3:19997800-20023200	Weak transcription	Spleen	Spleen
16	chr3:19998000-20017000	Weak transcription	HepG2	liver
17	chr3:19999600-20027600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr3:20003800-20023600	Weak transcription	Aorta	Aorta
19	chr3:20004000-20020400	Weak transcription	Esophagus	oesophagus
20	chr3:20007600-20016800	Weak transcription	Colonic Mucosa	Colon
21	chr3:20008600-20017000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr3:20008800-20016800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr3:20008800-20017800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr3:20008800-20035600	Weak transcription	Psoas Muscle	Psoas
25	chr3:20011800-20026400	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr3:20011800-20027400	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr3:20011800-20028000	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr3:20012000-20017200	Weak transcription	Colon Smooth Muscle	Colon
29	chr3:20012000-20017400	Weak transcription	Ovary	ovary
30	chr3:20012000-20021200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr3:20012000-20027800	Strong transcription	Primary B cells from peripheral blood	blood
32	chr3:20012000-20027800	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr3:20012200-20017200	Weak transcription	Brain Substantia Nigra	brain
34	chr3:20012200-20018000	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr3:20012200-20019200	Weak transcription	Fetal Heart	heart
36	chr3:20012200-20023600	Weak transcription	Brain Angular Gyrus	brain
37	chr3:20012200-20023600	Weak transcription	Gastric	stomach
38	chr3:20012200-20025600	Weak transcription	Pancreas	Pancrea
39	chr3:20012200-20026400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr3:20012400-20016800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr3:20012400-20017000	Weak transcription	Brain Hippocampus Middle	brain
42	chr3:20012400-20025600	Weak transcription	Stomach Mucosa	stomach
43	chr3:20012400-20027600	Strong transcription	Primary B cells from cord blood	blood
44	chr3:20012400-20033600	Weak transcription	Fetal Brain Male	brain
45	chr3:20012600-20016800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr3:20012600-20023200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr3:20013200-20019400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr3:20013400-20022200	Weak transcription	Lung	lung
49	chr3:20013800-20023800	Weak transcription	Right Ventricle	heart
50	chr3:20014000-20016800	Weak transcription	Muscle Satellite Cultured Cells	--

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