Variant report

Variant	rs12495962
Chromosome Location	chr3:158479326-158479327
allele	A/G
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	MYC	chr3:158479322-158479420	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:158464760..158466568-chr3:158477202..158479962,2	MCF-7	breast:
2	chr3:158477568..158480525-chr3:158482455..158485821,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000243675	TF binding region
ENSG00000118855	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs12489730	0.96[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs12491877	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12497488	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1430413	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1430414	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1560417	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1560418	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs16829365	0.87[ASN][1000 genomes]
rs17642769	0.95[ASN][1000 genomes]
rs17643171	0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs17643252	0.80[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs17643483	0.80[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs17643581	0.97[ASN][1000 genomes]
rs17643860	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17643917	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17699478	0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs17699526	0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs17699997	0.80[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs17700122	0.80[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs17700475	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2279561	0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2279562	0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2307064	0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2566347	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34690420	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3863076	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55678388	0.81[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs55705231	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs55717824	0.96[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs55776609	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56023805	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56078503	0.87[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs56105525	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56152025	0.80[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs56235582	0.83[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs56261306	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56318834	0.97[ASN][1000 genomes]
rs57262841	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59163359	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59173444	0.90[ASN][1000 genomes]
rs60203196	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61138408	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61794798	0.80[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs61794799	0.80[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs61794818	0.83[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs61794821	0.96[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs61794822	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61794833	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61794834	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61794835	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61794858	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61794859	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61796760	0.85[ASN][1000 genomes]
rs61796762	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61796764	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs61796766	0.83[ASN][1000 genomes]
rs61796768	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs61796770	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6441221	0.80[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs6761989	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6783610	0.80[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs6792908	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73158361	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7624420	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7624702	0.92[AMR][1000 genomes];0.91[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	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	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
4	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
5	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
6	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
7	nsv877692	chr3:158430706-158828643	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription 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	22 gene(s)	inside rSNPs	diseases
8	nsv1001450	chr3:158440011-158768399	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats 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	nsv536777	chr3:158440011-158768399	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Active TSS 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	22 gene(s)	inside rSNPs	diseases
10	nsv877693	chr3:158470321-158583004	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
11	nsv1006146	chr3:158475824-158625778	Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
12	nsv592123	chr3:158477796-158625128	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12495962	GFM1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158449800-158483000	Weak transcription	Fetal Heart	heart
2	chr3:158450800-158485400	Weak transcription	Psoas Muscle	Psoas
3	chr3:158451000-158484200	Weak transcription	Rectal Smooth Muscle	rectum
4	chr3:158451000-158485800	Weak transcription	Fetal Kidney	kidney
5	chr3:158453600-158486400	Weak transcription	Esophagus	oesophagus
6	chr3:158457400-158486000	Weak transcription	Right Ventricle	heart
7	chr3:158457800-158486200	Weak transcription	Pancreas	Pancrea
8	chr3:158460400-158486000	Weak transcription	Brain Hippocampus Middle	brain
9	chr3:158465400-158480000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr3:158465800-158480200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr3:158466000-158486000	Weak transcription	Aorta	Aorta
12	chr3:158466000-158486200	Weak transcription	Gastric	stomach
13	chr3:158466200-158482800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:158466200-158486200	Weak transcription	Brain Angular Gyrus	brain
15	chr3:158466200-158486200	Weak transcription	Fetal Brain Male	brain
16	chr3:158466600-158480000	Weak transcription	Fetal Brain Female	brain
17	chr3:158466600-158482600	Weak transcription	A549	lung
18	chr3:158466600-158485600	Weak transcription	Colonic Mucosa	Colon
19	chr3:158466600-158486200	Weak transcription	Brain Cingulate Gyrus	brain
20	chr3:158466800-158480200	Weak transcription	Fetal Muscle Leg	muscle
21	chr3:158466800-158480200	Weak transcription	Left Ventricle	heart
22	chr3:158466800-158486000	Weak transcription	Spleen	Spleen
23	chr3:158466800-158486200	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr3:158466800-158486200	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr3:158467000-158483000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr3:158467600-158480200	Weak transcription	Adipose Nuclei	Adipose
27	chr3:158467600-158485000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr3:158467600-158486000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr3:158467800-158480000	Weak transcription	Hela-S3	cervix
30	chr3:158468000-158483600	Weak transcription	Stomach Smooth Muscle	stomach
31	chr3:158468000-158486200	Weak transcription	Lung	lung
32	chr3:158468200-158488200	Weak transcription	Primary T cells from cord blood	blood
33	chr3:158468400-158483400	Weak transcription	Fetal Muscle Trunk	muscle
34	chr3:158468600-158483200	Weak transcription	Fetal Stomach	stomach
35	chr3:158468600-158485000	Weak transcription	Fetal Intestine Large	intestine
36	chr3:158472400-158486000	Weak transcription	Small Intestine	intestine
37	chr3:158473400-158484200	Weak transcription	Colon Smooth Muscle	Colon
38	chr3:158477800-158482600	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr3:158478400-158483200	Weak transcription	Osteobl	bone
40	chr3:158479000-158479600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr3:158479200-158480000	Enhancers	Fetal Lung	lung
42	chr3:158479200-158485600	Weak transcription	Fetal Intestine Small	intestine

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