Variant report

Variant	rs12426955
Chromosome Location	chr12:59313151-59313152
allele	G/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	MYC	chr12:59313059-59314590	Hela-S3	cervix:	n/a	chr12:59313589-59313604 chr12:59314410-59314419 chr12:59313591-59313600 chr12:59313592-59313599 chr12:59314408-59314421 chr12:59313590-59313601 chr12:59314409-59314420 chr12:59313590-59313601 chr12:59314410-59314419
2	MXI1	chr12:59312927-59314729	Hela-S3	cervix:	n/a	n/a
3	E2F6	chr12:59313149-59314852	H1-hESC	embryonic stem cell:	n/a	chr12:59313711-59313720 chr12:59314368-59314382
4	POLR2A	chr12:59312939-59313612	SK-N-MC	brain:	n/a	n/a
5	POLR2A	chr12:59313091-59314597	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr12:59312997-59314638	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr12:59313006-59314615	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr12:59313106-59314544	GM18505	blood:	n/a	n/a
9	MXI1	chr12:59312803-59315453	IMR90	lung:	n/a	n/a
10	TAF1	chr12:59312952-59313494	PFSK-1	brain:	n/a	n/a
11	ZKSCAN1	chr12:59312999-59313656	Hela-S3	cervix:	n/a	n/a
12	MAX	chr12:59312924-59314843	A549	lung:	n/a	chr12:59313589-59313604 chr12:59314410-59314419 chr12:59313591-59313600 chr12:59313592-59313599 chr12:59314408-59314421 chr12:59313590-59313601 chr12:59314409-59314420 chr12:59313590-59313601 chr12:59314410-59314419
13	POLR2A	chr12:59313050-59313574	IMR90	lung:	n/a	n/a
14	MAFK	chr12:59312977-59313781	IMR90	lung:	n/a	n/a
15	CREB1	chr12:59313034-59314680	HepG2	liver:	n/a	n/a
16	POLR2A	chr12:59313133-59314588	GM12892	blood:	n/a	n/a
17	POLR2A	chr12:59312969-59314504	GM12892	blood:	n/a	n/a
18	USF2	chr12:59313060-59313238	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr12:59313108-59313504	GM12892	blood:	n/a	n/a
20	POLR2A	chr12:59312970-59314686	Hela-S3	cervix:	n/a	n/a
21	MAX	chr12:59312922-59314624	Hela-S3	cervix:	n/a	chr12:59313589-59313604 chr12:59314410-59314419 chr12:59313591-59313600 chr12:59313592-59313599 chr12:59314408-59314421 chr12:59313590-59313601 chr12:59314409-59314420 chr12:59313590-59313601 chr12:59314410-59314419
22	POLR2A	chr12:59313089-59313594	GM12878	blood:	n/a	n/a
23	ZNF263	chr12:59313045-59314567	HEK293-T-REx	kidney:	n/a	chr12:59314127-59314136
24	CHD2	chr12:59313053-59314966	Hela-S3	cervix:	n/a	chr12:59313753-59313763
25	SIN3AK20	chr12:59312938-59313235	PFSK-1	brain:	n/a	n/a
26	POLR2A	chr12:59313091-59313509	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr12:59313017-59313690	GM12878	blood:	n/a	n/a
28	MYC	chr12:59312963-59313544	MCF10A-Er-Src	breast:	n/a	n/a
29	RCOR1	chr12:59313135-59313554	HepG2	liver:	n/a	n/a
30	MYC	chr12:59313125-59314869	MCF10A-Er-Src	breast:	n/a	chr12:59313589-59313604 chr12:59314410-59314419 chr12:59313591-59313600 chr12:59313592-59313599 chr12:59314408-59314421 chr12:59313590-59313601 chr12:59314409-59314420 chr12:59313590-59313601 chr12:59314410-59314419
31	RAD21	chr12:59313001-59314545	IMR90	lung:	n/a	chr12:59313005-59313017 chr12:59314429-59314443
32	GTF2F1	chr12:59312934-59313845	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr12:59313004-59313451	SK-N-MC	brain:	n/a	n/a
34	MAZ	chr12:59313062-59314610	Hela-S3	cervix:	n/a	chr12:59313589-59313604 chr12:59314410-59314419 chr12:59313591-59313600 chr12:59313592-59313599 chr12:59314408-59314421 chr12:59313590-59313601 chr12:59314409-59314420 chr12:59313590-59313601 chr12:59314410-59314419
35	MAFK	chr12:59312837-59314106	Hela-S3	cervix:	n/a	chr12:59312960-59312971
36	RCOR1	chr12:59312938-59314660	Hela-S3	cervix:	n/a	n/a
37	WRNIP1	chr12:59313144-59313452	GM12878	blood:	n/a	n/a
38	POLR2A	chr12:59309378-59314838	MCF10A-Er-Src	breast:	n/a	n/a
39	HA-E2F1	chr12:59313054-59314781	MCF-7	breast:	n/a	chr12:59313711-59313720 chr12:59314368-59314382
40	SMC3	chr12:59312951-59314846	Hela-S3	cervix:	n/a	n/a
41	RUNX3	chr12:59312981-59313711	GM12878	blood:	n/a	n/a
42	POLR2A	chr12:59313110-59314577	GM12878	blood:	n/a	n/a
43	POLR2A	chr12:59313124-59313610	GM12892	blood:	n/a	n/a
44	POLR2A	chr12:59312976-59314693	HepG2	liver:	n/a	n/a
45	POLR2A	chr12:59312840-59314844	HUVEC	blood vessel:	n/a	n/a
46	POLR2A	chr12:59312924-59313543	HUVEC	blood vessel:	n/a	n/a
47	TCF7L2	chr12:59313023-59314565	Hela-S3	cervix:	n/a	n/a
48	TBP	chr12:59312994-59313571	Hela-S3	cervix:	n/a	n/a
49	SIN3A	chr12:59313060-59314679	H1-hESC	embryonic stem cell:	n/a	chr12:59314409-59314418
50	TAF1	chr12:59313006-59313512	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:59306615..59312160-chr12:59312563..59315284,9	MCF-7	breast:

Variant related genes	Relation type
LRIG3	TF binding region
ENSG00000257443	TF binding region
ENSG00000139263	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs2291799	0.84[CHB][hapmap]
rs2291800	0.81[CHB][hapmap]
rs4760246	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7966785	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758311	chr12:59022729-59323045	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer 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	12 gene(s)	inside rSNPs	diseases
2	esv2759902	chr12:59022729-59323045	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv1043385	chr12:59149582-59758952	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv1067596	chr12:59167152-59764208	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv492251	chr12:59167152-59764208	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12426955	ESPL1	cis	cerebellum	SCAN
rs12426955	MBD6	cis	cerebellum	SCAN
rs12426955	PIP4K2C	cis	cerebellum	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:59303200-59313400	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr12:59308600-59314600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr12:59308800-59314600	Active TSS	Stomach Smooth Muscle	stomach
4	chr12:59309000-59314400	Active TSS	Breast Myoepithelial Primary Cells	Breast
5	chr12:59309000-59314600	Active TSS	HMEC	breast
6	chr12:59309200-59314600	Active TSS	Duodenum Mucosa	Duodenum
7	chr12:59309200-59314600	Active TSS	Fetal Intestine Small	intestine
8	chr12:59309200-59314600	Active TSS	Rectal Mucosa Donor 29	rectum
9	chr12:59309200-59314800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr12:59309200-59314800	Active TSS	Ovary	ovary
11	chr12:59309200-59315200	Active TSS	Duodenum Smooth Muscle	Duodenum
12	chr12:59309400-59315000	Active TSS	Fetal Muscle Trunk	muscle
13	chr12:59309800-59313400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr12:59309800-59314600	Active TSS	Skeletal Muscle Female	skeletal muscle
15	chr12:59310000-59313400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr12:59310000-59315000	Active TSS	Fetal Intestine Large	intestine
17	chr12:59310000-59315200	Active TSS	Rectal Smooth Muscle	rectum
18	chr12:59310400-59314400	Active TSS	Sigmoid Colon	Sigmoid Colon
19	chr12:59310400-59314800	Active TSS	Psoas Muscle	Psoas
20	chr12:59310400-59315200	Active TSS	Stomach Mucosa	stomach
21	chr12:59310600-59313600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr12:59310600-59314600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr12:59310600-59314600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr12:59310600-59314600	Active TSS	Fetal Stomach	stomach
25	chr12:59310600-59314600	Active TSS	NHLF	lung
26	chr12:59310600-59314800	Active TSS	Right Atrium	heart
27	chr12:59310600-59315000	Active TSS	Fetal Kidney	kidney
28	chr12:59310800-59314600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr12:59310800-59314600	Active TSS	NHEK	skin
30	chr12:59310800-59314800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr12:59310800-59314800	Active TSS	Aorta	Aorta
32	chr12:59310800-59315000	Active TSS	Pancreas	Pancrea
33	chr12:59311000-59313400	Active TSS	Fetal Muscle Leg	muscle
34	chr12:59311000-59314400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr12:59311000-59314600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr12:59311000-59314600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr12:59311000-59314600	Active TSS	HSMMtube	muscle
38	chr12:59311000-59314800	Active TSS	Colon Smooth Muscle	Colon
39	chr12:59311000-59314800	Active TSS	Right Ventricle	heart
40	chr12:59311000-59315000	Active TSS	Colonic Mucosa	Colon
41	chr12:59311200-59313200	Active TSS	Fetal Brain Female	brain
42	chr12:59311200-59314400	Active TSS	Fetal Lung	lung
43	chr12:59311200-59314400	Active TSS	Skeletal Muscle Male	skeletal muscle
44	chr12:59311200-59314400	Active TSS	Small Intestine	intestine
45	chr12:59311200-59314400	Active TSS	NH-A	brain
46	chr12:59311200-59314600	Active TSS	Brain Hippocampus Middle	brain
47	chr12:59311200-59314600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
48	chr12:59311200-59314600	Active TSS	GM12878-XiMat	blood
49	chr12:59311200-59314600	Active TSS	HUVEC	blood vessel
50	chr12:59311200-59314800	Active TSS	HSMM	muscle

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