Variant report

Variant	rs56139001
Chromosome Location	chr12:104699591-104699592
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	POLR2A	chr12:104698915-104700831	Hela-S3	cervix:	n/a	n/a
2	FOSL2	chr12:104699031-104700373	A549	lung:	n/a	n/a
3	SP1	chr12:104699009-104701770	A549	lung:	n/a	chr12:104700670-104700683
4	POLR2A	chr12:104698915-104702239	PANC-1	pancreas:	n/a	n/a
5	TCF12	chr12:104695268-104701849	A549	lung:	n/a	n/a
6	POLR2A	chr12:104696354-104701825	PANC-1	pancreas:	n/a	n/a
7	POLR2A	chr12:104696544-104702660	HepG2	liver:	n/a	n/a
8	POLR2A	chr12:104684682-104705657	A549	lung:	n/a	n/a
9	SIX5	chr12:104695288-104701950	A549	lung:	n/a	chr12:104700345-104700361 chr12:104699538-104699547 chr12:104698479-104698493 chr12:104700866-104700882
10	REST	chr12:104696446-104701824	A549	lung:	n/a	chr12:104698081-104698101 chr12:104697868-104697886 chr12:104698081-104698101 chr12:104698082-104698100 chr12:104698081-104698101
11	POLR2A	chr12:104699487-104700023	Hela-S3	cervix:	n/a	n/a
12	CEBPB	chr12:104699470-104700199	A549	lung:	n/a	n/a
13	SIN3AK20	chr12:104699471-104701756	A549	lung:	n/a	n/a
14	POLR2A	chr12:104698954-104699678	HUVEC	blood vessel:	n/a	n/a
15	POLR2A	chr12:104698980-104701758	HUVEC	blood vessel:	n/a	n/a
16	CTCF	chr12:104699480-104699630	AoAF	blood vessel:	n/a	n/a
17	POLR2A	chr12:104699587-104699632	K562	blood:	n/a	n/a
18	CEBPB	chr12:104699561-104700117	A549	lung:	n/a	n/a
19	POLR2A	chr12:104699142-104699786	HepG2	liver:	n/a	n/a
20	BCL3	chr12:104696463-104700456	A549	lung:	n/a	chr12:104697692-104697701 chr12:104697695-104697704
21	CTCF	chr12:104699480-104699630	AG10803	skin:	n/a	n/a
22	POLR2A	chr12:104699042-104700753	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr12:104697535-104699689	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:104696124..104698662-chr12:104698839..104702205,3	MCF-7	breast:

Variant related genes	Relation type
TXNRD1	TF binding region
ENSG00000255150	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs34244007	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34310509	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35090883	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35496411	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35730157	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35928066	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55717848	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60783408	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60836659	0.97[AFR][1000 genomes]
rs61116902	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899493	chr12:104548613-104703228	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Genic 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 target site	30 gene(s)	inside rSNPs	diseases
2	nsv899494	chr12:104561521-104806232	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1046606	chr12:104606617-104763734	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1038609	chr12:104613847-104764981	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv541587	chr12:104613847-104764981	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv1048075	chr12:104694799-104751460	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv541588	chr12:104694799-104751460	ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
8	nsv52994	chr12:104696286-104701777	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104683800-104723800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr12:104686200-104700600	Strong transcription	Dnd41	blood
3	chr12:104687200-104700600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:104691200-104702200	Transcr. at gene 5' and 3'	A549	lung
5	chr12:104691800-104703400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:104695800-104700800	Strong transcription	K562	blood
7	chr12:104696600-104701600	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr12:104697200-104700000	Strong transcription	HepG2	liver
9	chr12:104697200-104706200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr12:104698000-104699600	Weak transcription	Lung	lung
11	chr12:104698000-104700000	Enhancers	Right Ventricle	heart
12	chr12:104698000-104703000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr12:104698000-104703400	Weak transcription	Left Ventricle	heart
14	chr12:104698000-104704000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr12:104698000-104705000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr12:104698000-104707400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr12:104698000-104707600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr12:104698000-104707800	Weak transcription	Esophagus	oesophagus
19	chr12:104698000-104711400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr12:104698000-104716200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr12:104698200-104699600	Enhancers	Colon Smooth Muscle	Colon
22	chr12:104698200-104700200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr12:104698200-104700600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr12:104698200-104701800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr12:104698200-104702800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr12:104698200-104703000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr12:104698200-104703000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr12:104698200-104703600	Weak transcription	Pancreas	Pancrea
29	chr12:104698200-104704800	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr12:104698200-104705000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr12:104698200-104705000	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr12:104698200-104705000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr12:104698200-104705000	Weak transcription	Fetal Intestine Large	intestine
34	chr12:104698200-104706000	Weak transcription	Fetal Brain Male	brain
35	chr12:104698200-104706200	Weak transcription	Brain Germinal Matrix	brain
36	chr12:104698200-104708400	Genic enhancers	HUVEC	blood vessel
37	chr12:104698200-104708800	Weak transcription	Colonic Mucosa	Colon
38	chr12:104698400-104699600	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr12:104698400-104699600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr12:104698400-104699600	Weak transcription	Fetal Muscle Trunk	muscle
41	chr12:104698400-104699600	Weak transcription	Psoas Muscle	Psoas
42	chr12:104698400-104700000	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr12:104698400-104700000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
44	chr12:104698400-104700200	Enhancers	Primary T helper naive cells from peripheral blood	blood
45	chr12:104698400-104700600	Weak transcription	Fetal Intestine Small	intestine
46	chr12:104698400-104700600	Weak transcription	Stomach Smooth Muscle	stomach
47	chr12:104698400-104701000	Weak transcription	Fetal Kidney	kidney
48	chr12:104698400-104701000	Enhancers	Skeletal Muscle Female	skeletal muscle
49	chr12:104698400-104701600	Genic enhancers	Muscle Satellite Cultured Cells	--
50	chr12:104698400-104701600	Genic enhancers	Hela-S3	cervix

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