Variant report

Variant	rs7953876
Chromosome Location	chr12:124070843-124070844
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:124069627-124073859	K562	blood:	n/a	n/a
2	POLR2A	chr12:124068404-124070969	HepG2	liver:	n/a	n/a
3	POLR2A	chr12:124069683-124070910	HepG2	liver:	n/a	n/a
4	POLR2A	chr12:124068549-124070907	IMR90	lung:	n/a	n/a
5	MAZ	chr12:124068549-124070932	IMR90	lung:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:123892437..123894843-chr12:124070809..124073314,2	MCF-7	breast:
2	chr12:123755285..123757528-chr12:124068793..124071301,3	MCF-7	breast:
3	chr12:124067302..124072457-chr12:124084684..124088760,8	K562	blood:
4	chr12:124068831..124072178-chr12:124116882..124120107,5	K562	blood:
5	chr12:124067363..124072745-chr12:124084857..124088217,7	K562	blood:
6	chr12:123941578..123944282-chr12:124067320..124071098,9	MCF-7	breast:
7	chr12:123846861..123850261-chr12:124066655..124071408,9	MCF-7	breast:
8	chr12:124015697..124018727-chr12:124070609..124072770,3	K562	blood:
9	chr12:124016749..124018606-chr12:124069216..124071514,2	K562	blood:
10	chr12:123847713..123850022-chr12:124067528..124071055,3	MCF-7	breast:
11	chr12:123872778..123876196-chr12:124065295..124071344,6	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000247373	TF binding region
ENSG00000184209	Chromatin interaction
ENSG00000183955	Chromatin interaction
ENSG00000188026	Chromatin interaction
ENSG00000111328	Chromatin interaction
ENSG00000256092	Chromatin interaction
ENSG00000111364	Chromatin interaction
ENSG00000111358	Chromatin interaction
ENSG00000139697	Chromatin interaction
ENSG00000111361	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1050443	0.92[EUR][1000 genomes]
rs1050448	0.84[EUR][1000 genomes]
rs1050449	0.84[EUR][1000 genomes]
rs1056132	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11057301	0.82[EUR][1000 genomes]
rs11833889	0.87[EUR][1000 genomes]
rs12809853	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12816883	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12829500	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs15587	0.87[EUR][1000 genomes]
rs16917551	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3190835	0.85[EUR][1000 genomes]
rs3204541	0.87[EUR][1000 genomes]
rs34097324	0.87[EUR][1000 genomes]
rs34369761	0.83[EUR][1000 genomes]
rs34514002	0.87[EUR][1000 genomes]
rs35064645	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35708602	0.87[EUR][1000 genomes]
rs35867744	0.87[EUR][1000 genomes]
rs36002329	0.98[EUR][1000 genomes]
rs3850952	0.81[EUR][1000 genomes]
rs4930704	0.85[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4930709	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4930712	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4930713	0.82[EUR][1000 genomes]
rs4930714	0.82[EUR][1000 genomes]
rs55705511	0.85[EUR][1000 genomes]
rs56213464	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56675602	0.87[EUR][1000 genomes]
rs59126974	0.87[EUR][1000 genomes]
rs6488877	0.86[ASN][1000 genomes]
rs6488884	0.83[EUR][1000 genomes]
rs66494087	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66694750	0.87[EUR][1000 genomes]
rs68163141	0.85[EUR][1000 genomes]
rs7137473	0.87[EUR][1000 genomes]
rs7139162	0.87[EUR][1000 genomes]
rs71458807	0.92[EUR][1000 genomes]
rs71458808	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7308304	0.87[EUR][1000 genomes]
rs7309292	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7313207	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7313751	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7398935	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7956299	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7962151	0.86[ASN][1000 genomes]
rs7963804	0.86[ASN][1000 genomes]
rs7972380	0.82[EUR][1000 genomes]
rs7973766	0.83[EUR][1000 genomes]
rs7979561	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038841	chr12:123757305-124087671	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv541622	chr12:123757305-124087671	Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv1050598	chr12:123991646-124214332	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv541623	chr12:123991646-124214332	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv498024	chr12:123994372-124459856	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
6	esv2422416	chr12:124009676-124085689	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	nsv1042181	chr12:124037400-124152950	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7953876	TCTN2	cis	Adipose Subcutaneous	GTEx
rs7953876	TCTN2	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124067600-124071400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr12:124070000-124071000	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr12:124070000-124071400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr12:124070000-124071600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr12:124070000-124071800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
6	chr12:124070000-124073000	Weak transcription	Lung	lung
7	chr12:124070000-124073200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:124070000-124073200	Weak transcription	Esophagus	oesophagus
9	chr12:124070000-124085800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr12:124070200-124071000	Enhancers	Primary T cells fromperipheralblood	blood
11	chr12:124070200-124071000	Enhancers	Placenta	Placenta
12	chr12:124070200-124071200	Weak transcription	Fetal Muscle Trunk	muscle
13	chr12:124070200-124071200	Enhancers	Left Ventricle	heart
14	chr12:124070200-124072000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr12:124070200-124073200	Weak transcription	Aorta	Aorta
16	chr12:124070200-124073400	Weak transcription	Stomach Mucosa	stomach
17	chr12:124070400-124071000	Enhancers	Primary hematopoietic stem cells	blood
18	chr12:124070400-124071000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr12:124070400-124071000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr12:124070400-124071000	Enhancers	Thymus	Thymus
21	chr12:124070400-124071200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
22	chr12:124070400-124071200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr12:124070400-124071200	Enhancers	Liver	Liver
24	chr12:124070400-124071200	Weak transcription	Brain Angular Gyrus	brain
25	chr12:124070400-124071200	Enhancers	Brain Anterior Caudate	brain
26	chr12:124070400-124071200	Weak transcription	Fetal Kidney	kidney
27	chr12:124070400-124071400	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr12:124070400-124071400	Enhancers	Fetal Heart	heart
29	chr12:124070400-124071800	Enhancers	Primary T helper naive cells from peripheral blood	blood
30	chr12:124070400-124071800	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr12:124070400-124072000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr12:124070400-124072200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr12:124070400-124072400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr12:124070400-124072400	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr12:124070400-124072400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr12:124070400-124072600	Enhancers	Primary T killer memory cells from peripheral blood	blood
37	chr12:124070400-124072600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr12:124070400-124072600	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr12:124070400-124072600	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr12:124070400-124073200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr12:124070400-124073200	Weak transcription	Gastric	stomach
42	chr12:124070400-124073200	Weak transcription	Pancreas	Pancrea
43	chr12:124070400-124073800	Genic enhancers	Stomach Smooth Muscle	stomach
44	chr12:124070400-124076400	Weak transcription	Ovary	ovary
45	chr12:124070400-124076600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr12:124070600-124071000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr12:124070600-124071000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr12:124070600-124071000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr12:124070600-124071000	Enhancers	Adipose Nuclei	Adipose
50	chr12:124070600-124071000	Enhancers	Fetal Brain Male	brain

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