Variant report

Variant	rs36002329
Chromosome Location	chr12:124070612-124070613
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:21)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:21 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:124070122-124070757	GM12892	blood:	n/a	n/a
2	POLR2A	chr12:124068520-124070709	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr12:124069627-124073859	K562	blood:	n/a	n/a
4	POLR2A	chr12:124070574-124070785	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr12:124069686-124070761	GM12878	blood:	n/a	n/a
6	CEBPB	chr12:124070004-124070702	IMR90	lung:	n/a	chr12:124070264-124070281 chr12:124070266-124070277 chr12:124070265-124070276
7	MXI1	chr12:124068488-124070795	IMR90	lung:	n/a	n/a
8	POLR2A	chr12:124069625-124070734	PFSK-1	brain:	n/a	n/a
9	POLR2A	chr12:124069888-124070634	K562	blood:	n/a	n/a
10	POLR2A	chr12:124068404-124070969	HepG2	liver:	n/a	n/a
11	POLR2A	chr12:124070117-124070785	HepG2	liver:	n/a	n/a
12	POLR2A	chr12:124070552-124070807	HepG2	liver:	n/a	n/a
13	POLR2A	chr12:124068344-124070778	MCF10A-Er-Src	breast:	n/a	n/a
14	POLR2A	chr12:124069683-124070910	HepG2	liver:	n/a	n/a
15	RFX5	chr12:124070425-124070669	K562	blood:	n/a	n/a
16	TBL1XR1	chr12:124070185-124070624	K562	blood:	n/a	n/a
17	CHD1	chr12:124068312-124070779	IMR90	lung:	n/a	chr12:124069693-124069700
18	IRF1	chr12:124070539-124070628	K562	blood:	n/a	n/a
19	JUN	chr12:124068570-124070748	K562	blood:	n/a	chr12:124070434-124070446
20	POLR2A	chr12:124068549-124070907	IMR90	lung:	n/a	n/a
21	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	chr12:123755285..123757528-chr12:124068793..124071301,3	MCF-7	breast:
2	chr12:124067567..124070616-chr12:124116717..124118360,3	K562	blood:
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
ENSG00000139697	Chromatin interaction
ENSG00000111328	Chromatin interaction
ENSG00000111358	Chromatin interaction
ENSG00000111364	Chromatin interaction
ENSG00000188026	Chromatin interaction
ENSG00000184209	Chromatin interaction
ENSG00000183955	Chromatin interaction
ENSG00000256092	Chromatin interaction
ENSG00000111361	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1050443	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1050448	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1050449	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1056132	0.99[EUR][1000 genomes]
rs11057301	0.81[EUR][1000 genomes]
rs11833889	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12809853	0.94[EUR][1000 genomes]
rs12816883	0.86[EUR][1000 genomes]
rs12829500	0.95[EUR][1000 genomes]
rs15587	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16917551	0.99[EUR][1000 genomes]
rs3190835	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3204541	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34097324	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34369761	0.81[EUR][1000 genomes]
rs34514002	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35016092	0.89[ASN][1000 genomes]
rs35064645	0.99[EUR][1000 genomes]
rs35708602	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35867744	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3850952	0.80[EUR][1000 genomes]
rs4930709	0.94[EUR][1000 genomes]
rs4930712	0.99[EUR][1000 genomes]
rs4930713	0.81[EUR][1000 genomes]
rs4930714	0.81[EUR][1000 genomes]
rs55705511	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56213464	0.94[EUR][1000 genomes]
rs56675602	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59126974	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6488878	0.89[ASN][1000 genomes]
rs6488884	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs66494087	0.98[EUR][1000 genomes]
rs66694750	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68163141	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7137473	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7139162	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71458807	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71458808	0.94[EUR][1000 genomes]
rs7308304	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7309292	0.99[EUR][1000 genomes]
rs7313207	0.97[EUR][1000 genomes]
rs7953876	0.98[EUR][1000 genomes]
rs7959714	0.89[ASN][1000 genomes]
rs7972380	0.81[EUR][1000 genomes]
rs7973766	0.81[EUR][1000 genomes]
rs7979561	0.97[EUR][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
rs36002329	TCTN2	cis	Adipose Subcutaneous	GTEx
rs36002329	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	chr12:124067400-124070800	Active TSS	NHLF	lung
2	chr12:124067600-124071400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr12:124069600-124070800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr12:124069800-124070800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr12:124069800-124070800	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr12:124069800-124070800	Flanking Active TSS	HUVEC	blood vessel
7	chr12:124069800-124070800	Flanking Active TSS	NH-A	brain
8	chr12:124070000-124070800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr12:124070000-124070800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr12:124070000-124070800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr12:124070000-124070800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr12:124070000-124070800	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr12:124070000-124070800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr12:124070000-124070800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
15	chr12:124070000-124070800	Flanking Active TSS	Hela-S3	cervix
16	chr12:124070000-124070800	Flanking Active TSS	HMEC	breast
17	chr12:124070000-124071000	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr12:124070000-124071400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr12:124070000-124071600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr12:124070000-124071800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr12:124070000-124073000	Weak transcription	Lung	lung
22	chr12:124070000-124073200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr12:124070000-124073200	Weak transcription	Esophagus	oesophagus
24	chr12:124070000-124085800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr12:124070200-124070800	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr12:124070200-124070800	Enhancers	Brain Substantia Nigra	brain
27	chr12:124070200-124070800	Flanking Active TSS	HepG2	liver
28	chr12:124070200-124070800	Transcr. at gene 5' and 3'	K562	blood
29	chr12:124070200-124071000	Enhancers	Primary T cells fromperipheralblood	blood
30	chr12:124070200-124071000	Enhancers	Placenta	Placenta
31	chr12:124070200-124071200	Weak transcription	Fetal Muscle Trunk	muscle
32	chr12:124070200-124071200	Enhancers	Left Ventricle	heart
33	chr12:124070200-124072000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr12:124070200-124073200	Weak transcription	Aorta	Aorta
35	chr12:124070200-124073400	Weak transcription	Stomach Mucosa	stomach
36	chr12:124070400-124070800	Active TSS	ES-I3 Cell Line	embryonic stem cell
37	chr12:124070400-124070800	Active TSS	iPS-20b Cell Line	embryonic stem cell
38	chr12:124070400-124070800	Enhancers	Primary B cells from cord blood	blood
39	chr12:124070400-124070800	Enhancers	Brain Hippocampus Middle	brain
40	chr12:124070400-124070800	Enhancers	Colon Smooth Muscle	Colon
41	chr12:124070400-124070800	Enhancers	Duodenum Smooth Muscle	Duodenum
42	chr12:124070400-124070800	Enhancers	Fetal Brain Female	brain
43	chr12:124070400-124070800	Enhancers	Rectal Mucosa Donor 31	rectum
44	chr12:124070400-124070800	Enhancers	Skeletal Muscle Male	skeletal muscle
45	chr12:124070400-124070800	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr12:124070400-124071000	Enhancers	Primary hematopoietic stem cells	blood
47	chr12:124070400-124071000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr12:124070400-124071000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
49	chr12:124070400-124071000	Enhancers	Thymus	Thymus
50	chr12:124070400-124071200	Enhancers	Primary T regulatory cells fromperipheralblood	blood

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