Variant report

Variant	rs786454
Chromosome Location	chr12:124055358-124055359
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:124047707..124050611-chr12:124054919..124057365,3	MCF-7	breast:
2	chr12:124041024..124043349-chr12:124054707..124057427,2	MCF-7	breast:
3	chr12:124017387..124020298-chr12:124054468..124057519,3	MCF-7	breast:
4	chr12:124054266..124056450-chr12:124065485..124066989,2	MCF-7	breast:
5	chr1:150334954..150337894-chr12:124054865..124057568,2	MCF-7	breast:
6	chr12:124014995..124016623-chr12:124054786..124056310,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163125	Chromatin interaction
ENSG00000188026	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1057879	0.85[ASN][1000 genomes]
rs10846528	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11057297	0.96[ASN][1000 genomes]
rs11057300	0.81[ASN][1000 genomes]
rs11057301	0.81[ASN][1000 genomes]
rs2048615	0.85[ASN][1000 genomes]
rs2333831	0.85[ASN][1000 genomes]
rs28371124	0.85[ASN][1000 genomes]
rs28408980	0.91[ASN][1000 genomes]
rs28430750	0.85[ASN][1000 genomes]
rs28454032	0.82[ASN][1000 genomes]
rs28478446	0.85[ASN][1000 genomes]
rs28497190	0.85[ASN][1000 genomes]
rs28701527	0.85[ASN][1000 genomes]
rs28707421	0.85[ASN][1000 genomes]
rs28712858	0.85[ASN][1000 genomes]
rs28741988	0.85[ASN][1000 genomes]
rs28834793	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34369761	0.81[ASN][1000 genomes]
rs3850952	0.81[ASN][1000 genomes]
rs4456350	0.81[AFR][1000 genomes]
rs4930713	0.81[ASN][1000 genomes]
rs4930714	0.81[ASN][1000 genomes]
rs5027860	0.82[ASN][1000 genomes]
rs71458805	0.81[ASN][1000 genomes]
rs7315326	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs786444	0.91[AFR][1000 genomes]
rs7959727	0.91[ASN][1000 genomes]
rs7965334	0.82[ASN][1000 genomes]
rs7972380	0.81[ASN][1000 genomes]
rs9919	0.81[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs786454	TCTN2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124054200-124055400	Enhancers	Dnd41	blood
2	chr12:124054600-124056000	Enhancers	ES-I3 Cell Line	embryonic stem cell
3	chr12:124054600-124056200	Enhancers	Fetal Thymus	thymus
4	chr12:124054600-124056400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr12:124054800-124055400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr12:124054800-124055400	Flanking Active TSS	HepG2	liver
7	chr12:124054800-124055800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr12:124054800-124056000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr12:124054800-124056000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr12:124054800-124056000	Enhancers	K562	blood
11	chr12:124054800-124056200	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr12:124054800-124056200	Enhancers	Thymus	Thymus
13	chr12:124054800-124056200	Enhancers	HUVEC	blood vessel
14	chr12:124054800-124056200	Enhancers	NHEK	skin
15	chr12:124055000-124056200	Weak transcription	NHDF-Ad	bronchial
16	chr12:124055000-124056400	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr12:124055000-124056400	Enhancers	Osteobl	bone
18	chr12:124055000-124065000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr12:124055000-124067400	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr12:124055200-124055400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr12:124055200-124055800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr12:124055200-124056200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr12:124055200-124056400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr12:124055200-124060800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr12:124055200-124068000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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