Variant report

Variant	rs12319420
Chromosome Location	chr12:29672878-29672879
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	CTCF	chr12:29672760-29672910	BE2_C	brain:	n/a	n/a
2	CTCF	chr12:29672309-29673163	SK-N-SH	brain:	n/a	chr12:29672706-29672724 chr12:29672709-29672717 chr12:29672708-29672729 chr12:29672709-29672722 chr12:29672707-29672723
3	CTCF	chr12:29672606-29672923	MCF-7	breast:	n/a	chr12:29672706-29672724 chr12:29672709-29672717 chr12:29672708-29672729 chr12:29672709-29672722 chr12:29672707-29672723
4	RAD21	chr12:29672475-29673019	MCF-7	breast:	n/a	chr12:29672707-29672726
5	RAD21	chr12:29672520-29672888	GM12878	blood:	n/a	chr12:29672707-29672726
6	CTCF	chr12:29672000-29673246	A549	lung:	n/a	chr12:29672706-29672724 chr12:29672709-29672717 chr12:29672708-29672729 chr12:29672709-29672722 chr12:29672707-29672723
7	RAD21	chr12:29672508-29672984	A549	lung:	n/a	chr12:29672707-29672726
8	SMC3	chr12:29672439-29672912	HepG2	liver:	n/a	chr12:29672708-29672716 chr12:29672708-29672722
9	CTCF	chr12:29672503-29672923	K562	blood:	n/a	chr12:29672706-29672724 chr12:29672709-29672717 chr12:29672708-29672729 chr12:29672709-29672722 chr12:29672707-29672723
10	RAD21	chr12:29672399-29673032	HCT-116	colon:	n/a	chr12:29672707-29672726
11	RAD21	chr12:29672551-29672896	K562	blood:	n/a	chr12:29672707-29672726
12	SMC3	chr12:29672505-29673099	GM12878	blood:	n/a	chr12:29672708-29672716 chr12:29672708-29672722
13	RAD21	chr12:29672513-29672945	H1-hESC	embryonic stem cell:	n/a	chr12:29672707-29672726
14	ARID3A	chr12:29672607-29672895	HepG2	liver:	n/a	n/a
15	RFX5	chr12:29672570-29672930	Hela-S3	cervix:	n/a	n/a
16	RAD21	chr12:29672484-29672931	SK-N-SH_RA	brain:	n/a	chr12:29672707-29672726
17	CTCF	chr12:29672479-29672891	A549	lung:	n/a	chr12:29672706-29672724 chr12:29672709-29672717 chr12:29672708-29672729 chr12:29672709-29672722 chr12:29672707-29672723
18	RAD21	chr12:29672390-29673035	Hela-S3	cervix:	n/a	chr12:29672707-29672726
19	CTCF	chr12:29672740-29672890	HCM	heart:	n/a	n/a
20	RAD21	chr12:29672186-29673191	SK-N-SH	brain:	n/a	chr12:29672707-29672726
21	SMC3	chr12:29672461-29672887	K562	blood:	n/a	chr12:29672708-29672716 chr12:29672708-29672722
22	RAD21	chr12:29672423-29673006	ECC-1	luminal epithelium:	n/a	chr12:29672707-29672726
23	RAD21	chr12:29672467-29672994	GM12878	blood:	n/a	chr12:29672707-29672726
24	RAD21	chr12:29672402-29673032	HCT-116	colon:	n/a	chr12:29672707-29672726
25	RAD21	chr12:29672482-29672940	MCF-7	breast:	n/a	chr12:29672707-29672726
26	CTCF	chr12:29672535-29672890	A549	lung:	n/a	chr12:29672706-29672724 chr12:29672709-29672717 chr12:29672708-29672729 chr12:29672709-29672722 chr12:29672707-29672723
27	RAD21	chr12:29672494-29673004	ECC-1	luminal epithelium:	n/a	chr12:29672707-29672726
28	SMC3	chr12:29672423-29673040	Hela-S3	cervix:	n/a	chr12:29672708-29672716 chr12:29672708-29672722
29	RAD21	chr12:29672430-29673039	IMR90	lung:	n/a	chr12:29672707-29672726
30	RAD21	chr12:29672490-29672970	HepG2	liver:	n/a	chr12:29672707-29672726
31	CTCF	chr12:29672539-29672936	MCF-7	breast:	n/a	chr12:29672707-29672723 chr12:29672706-29672724 chr12:29672709-29672722 chr12:29672708-29672729 chr12:29672709-29672717
32	ZNF143	chr12:29672566-29672884	GM12878	blood:	n/a	n/a
33	CTCF	chr12:29672555-29672949	T-47D	breast:	n/a	chr12:29672706-29672724 chr12:29672709-29672717 chr12:29672708-29672729 chr12:29672709-29672722 chr12:29672707-29672723
34	RAD21	chr12:29672508-29672947	H1-hESC	embryonic stem cell:	n/a	chr12:29672707-29672726
35	CTCF	chr12:29672397-29673001	HCT-116	colon:	n/a	chr12:29672706-29672724 chr12:29672709-29672717 chr12:29672708-29672729 chr12:29672709-29672722 chr12:29672707-29672723
36	RAD21	chr12:29672607-29672910	SK-N-SH_RA	brain:	n/a	chr12:29672707-29672726
37	CTCF	chr12:29672484-29672915	IMR90	lung:	n/a	chr12:29672706-29672724 chr12:29672709-29672717 chr12:29672708-29672729 chr12:29672709-29672722 chr12:29672707-29672723
38	CTCF	chr12:29672513-29672943	GM12878	blood:	n/a	chr12:29672706-29672724 chr12:29672709-29672717 chr12:29672708-29672729 chr12:29672709-29672722 chr12:29672707-29672723
39	SMC3	chr12:29672406-29672986	SK-N-SH	brain:	n/a	chr12:29672708-29672716 chr12:29672708-29672722
40	ZNF384	chr12:29672865-29672927	GM12878	blood:	n/a	n/a
41	RAD21	chr12:29672495-29673060	A549	lung:	n/a	chr12:29672707-29672726
42	POLR2A	chr12:29672841-29672929	HUVEC	blood vessel:	n/a	n/a
43	BRCA1	chr12:29672594-29672918	Hela-S3	cervix:	n/a	n/a
44	RAD21	chr12:29672553-29672939	HepG2	liver:	n/a	chr12:29672707-29672726

Variant related genes	Relation type
TMTC1	TF binding region

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11050264	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11050265	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12164837	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12227259	1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12297627	1.00[TSI][hapmap]
rs12299179	1.00[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053641	chr12:29268813-29854413	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers 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	40 gene(s)	inside rSNPs	diseases
2	nsv469190	chr12:29612425-29811471	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv557917	chr12:29612425-29811471	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29600600-29675600	Weak transcription	Psoas Muscle	Psoas
2	chr12:29650400-29699000	Weak transcription	Right Ventricle	heart
3	chr12:29652200-29673200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr12:29656200-29673800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr12:29657200-29675600	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr12:29658000-29680200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr12:29658000-29681200	Weak transcription	Colon Smooth Muscle	Colon
8	chr12:29658400-29690200	Weak transcription	HMEC	breast
9	chr12:29658600-29678800	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr12:29660800-29690000	Weak transcription	NHDF-Ad	bronchial
11	chr12:29665400-29725400	Weak transcription	Brain Cingulate Gyrus	brain
12	chr12:29665800-29675000	Weak transcription	Fetal Heart	heart
13	chr12:29667000-29680200	Weak transcription	Fetal Kidney	kidney
14	chr12:29667200-29695600	Weak transcription	Ovary	ovary
15	chr12:29668600-29674600	Weak transcription	Fetal Muscle Trunk	muscle
16	chr12:29668600-29690000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr12:29668600-29695800	Weak transcription	Aorta	Aorta
18	chr12:29668800-29706000	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr12:29668800-29716600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr12:29669800-29673600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr12:29670000-29673400	Weak transcription	Brain Anterior Caudate	brain
22	chr12:29670000-29674000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr12:29670000-29674000	Strong transcription	Muscle Satellite Cultured Cells	--
24	chr12:29670600-29675000	Weak transcription	HSMM	muscle
25	chr12:29670600-29677400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr12:29670600-29680200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr12:29670600-29687000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr12:29670600-29687800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr12:29670600-29697400	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr12:29670600-29699000	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr12:29671000-29688000	Weak transcription	Fetal Muscle Leg	muscle
32	chr12:29671000-29697200	Weak transcription	Spleen	Spleen
33	chr12:29671600-29674600	Weak transcription	Stomach Smooth Muscle	stomach
34	chr12:29671600-29681000	Weak transcription	Adipose Nuclei	Adipose
35	chr12:29671600-29681000	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr12:29671600-29695400	Weak transcription	Fetal Stomach	stomach
37	chr12:29671600-29697200	Weak transcription	Left Ventricle	heart
38	chr12:29672200-29673800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr12:29672200-29680200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr12:29672400-29675800	Enhancers	Hela-S3	cervix
41	chr12:29672600-29673200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr12:29672600-29686000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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