Variant report

Variant	rs16847123
Chromosome Location	chr3:158416137-158416138
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF143	chr3:158416098-158416164	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:158415825..158417591-chr3:158438376..158440279,2	MCF-7	breast:
2	chr3:158415231..158418143-chr3:158424169..158428339,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272087	TF binding region

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10276	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1051109	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10936149	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12185969	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12488114	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12488447	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12494750	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12629635	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12630515	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12633674	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12637295	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12639329	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16829122	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16829290	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16829314	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16847125	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1946557	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2082158	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2082159	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2291595	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2363658	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3773712	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4334688	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4459938	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4679831	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4680448	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4680454	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4680455	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4680456	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6765967	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6768636	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6801874	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73156423	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73156425	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73156426	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73156428	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73156437	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73156439	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73156451	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73156455	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73156465	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73156478	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73156488	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73156489	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73156490	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73156491	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73156492	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73156495	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73156496	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7617983	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7648050	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002378	chr3:157715428-158673414	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv1004124	chr3:158146715-158808638	Genic enhancers Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS 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 target site	37 gene(s)	inside rSNPs	diseases
3	esv2763312	chr3:158193512-158420588	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv869644	chr3:158308783-158426343	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv530059	chr3:158332590-159147549	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats 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	31 gene(s)	inside rSNPs	diseases
6	nsv1014255	chr3:158358860-158768542	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv532665	chr3:158370013-158754245	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
8	nsv948755	chr3:158388780-158672287	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS 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	22 gene(s)	inside rSNPs	diseases
9	nsv1007141	chr3:158415840-158433128	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16847123	MLF1	cis	Heart Left Ventricle	GTEx
rs16847123	RP11-538P18.2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158390400-158416800	Weak transcription	Aorta	Aorta
2	chr3:158390400-158428600	Weak transcription	Brain Cingulate Gyrus	brain
3	chr3:158390600-158427400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:158390800-158416800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr3:158390800-158425400	Weak transcription	Fetal Brain Female	brain
6	chr3:158390800-158427000	Weak transcription	Brain Angular Gyrus	brain
7	chr3:158390800-158427400	Weak transcription	Esophagus	oesophagus
8	chr3:158390800-158427400	Weak transcription	Lung	lung
9	chr3:158390800-158429400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr3:158390800-158430200	Weak transcription	Brain Hippocampus Middle	brain
11	chr3:158390800-158430400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr3:158390800-158430800	Weak transcription	Right Ventricle	heart
13	chr3:158390800-158430800	Weak transcription	Stomach Mucosa	stomach
14	chr3:158390800-158432800	Weak transcription	Spleen	Spleen
15	chr3:158390800-158444200	Weak transcription	Gastric	stomach
16	chr3:158390800-158445400	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr3:158391000-158418600	Weak transcription	Fetal Brain Male	brain
18	chr3:158391000-158421000	Weak transcription	Fetal Heart	heart
19	chr3:158391000-158427200	Weak transcription	NHEK	skin
20	chr3:158391000-158427400	Weak transcription	Pancreas	Pancrea
21	chr3:158391000-158429200	Weak transcription	Colon Smooth Muscle	Colon
22	chr3:158391000-158430600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr3:158391000-158438800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr3:158395800-158420800	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr3:158395800-158423000	Weak transcription	Fetal Stomach	stomach
26	chr3:158396200-158418400	Weak transcription	Brain Germinal Matrix	brain
27	chr3:158397000-158429200	Weak transcription	Ovary	ovary
28	chr3:158397000-158443400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr3:158397000-158448000	Weak transcription	Thymus	Thymus
30	chr3:158397800-158425200	Weak transcription	HSMMtube	muscle
31	chr3:158399600-158445400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr3:158400600-158429000	Weak transcription	Brain Substantia Nigra	brain
33	chr3:158403600-158438600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr3:158403800-158420800	Weak transcription	HMEC	breast
35	chr3:158408000-158417800	Strong transcription	Fetal Intestine Large	intestine
36	chr3:158408400-158430200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr3:158408400-158443000	Weak transcription	HepG2	liver
38	chr3:158408600-158419400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr3:158408800-158422400	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr3:158409000-158429800	Weak transcription	Small Intestine	intestine
41	chr3:158409200-158421200	Weak transcription	Psoas Muscle	Psoas
42	chr3:158409200-158427400	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr3:158409400-158425400	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr3:158409400-158425600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr3:158409400-158426200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr3:158409400-158426800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr3:158409400-158427200	Weak transcription	Brain Anterior Caudate	brain
48	chr3:158409600-158417600	Weak transcription	NHDF-Ad	bronchial
49	chr3:158409800-158439000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr3:158410000-158424200	Weak transcription	Rectal Mucosa Donor 31	rectum

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