Variant report

Variant	rs786443
Chromosome Location	chr12:124063891-124063892
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:124061690..124064565-chr12:124067348..124070635,4	MCF-7	breast:
2	chr12:124018351..124020362-chr12:124063140..124065356,2	MCF-7	breast:
3	chr12:124063601..124065298-chr12:124067381..124068906,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000247373	Chromatin interaction
ENSG00000086598	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10846531	0.84[ASN][1000 genomes]
rs10846535	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11057307	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11057320	0.80[EUR][1000 genomes]
rs11615300	0.81[EUR][1000 genomes]
rs1515814	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2048802	0.84[ASN][1000 genomes]
rs3748268	0.84[ASN][1000 genomes]
rs3748269	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4040225	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4456350	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6488883	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6551	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7134896	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7302183	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7313628	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs786422	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786423	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786425	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786441	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs786444	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786445	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786447	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786448	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786449	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786452	0.90[ASN][1000 genomes]
rs7966882	0.83[EUR][1000 genomes]
rs7972413	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs884892	0.84[ASN][1000 genomes]
rs908373	0.81[EUR][1000 genomes];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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs786443	TCTN2	cis	Adipose Subcutaneous	GTEx
rs786443	TCTN2	cis	Artery Tibial	GTEx

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124055000-124065000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr12:124055000-124067400	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr12:124055200-124068000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr12:124055400-124067800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr12:124056000-124066600	Weak transcription	Fetal Muscle Leg	muscle
6	chr12:124056000-124066600	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr12:124056000-124067000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr12:124056000-124067800	Weak transcription	Lung	lung
9	chr12:124056200-124064800	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr12:124056200-124065000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr12:124056200-124066600	Weak transcription	Thymus	Thymus
12	chr12:124056200-124067000	Weak transcription	Duodenum Mucosa	Duodenum
13	chr12:124056200-124067200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr12:124056400-124065200	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr12:124056400-124065400	Weak transcription	Osteobl	bone
16	chr12:124056400-124066600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr12:124056400-124066600	Weak transcription	Adipose Nuclei	Adipose
18	chr12:124056400-124066600	Weak transcription	Brain Anterior Caudate	brain
19	chr12:124056400-124066600	Weak transcription	K562	blood
20	chr12:124056400-124066800	Weak transcription	Brain Hippocampus Middle	brain
21	chr12:124056400-124066800	Weak transcription	Stomach Smooth Muscle	stomach
22	chr12:124056400-124067000	Weak transcription	NHDF-Ad	bronchial
23	chr12:124056400-124067400	Weak transcription	HSMMtube	muscle
24	chr12:124056800-124066600	Weak transcription	Dnd41	blood
25	chr12:124058800-124066600	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr12:124058800-124067000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr12:124059200-124066800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr12:124059200-124066800	Weak transcription	Spleen	Spleen
29	chr12:124059200-124067200	Weak transcription	Brain Germinal Matrix	brain
30	chr12:124059400-124066600	Weak transcription	Liver	Liver
31	chr12:124059400-124067000	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr12:124059400-124067200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr12:124059800-124066600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr12:124059800-124066800	Weak transcription	Fetal Kidney	kidney
35	chr12:124060000-124066800	Weak transcription	Ovary	ovary
36	chr12:124060000-124067000	Weak transcription	NHLF	lung
37	chr12:124060400-124066000	Weak transcription	Primary B cells from cord blood	blood
38	chr12:124060400-124066600	Weak transcription	HSMM	muscle
39	chr12:124060400-124066800	Weak transcription	Gastric	stomach
40	chr12:124060600-124066800	Weak transcription	GM12878-XiMat	blood
41	chr12:124061000-124064400	Strong transcription	Fetal Stomach	stomach
42	chr12:124061000-124066000	Weak transcription	Fetal Muscle Trunk	muscle
43	chr12:124061000-124066600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr12:124061000-124066800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr12:124061000-124066800	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr12:124061000-124067000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr12:124061200-124066800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr12:124061200-124067000	Weak transcription	Fetal Lung	lung
49	chr12:124061200-124067200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr12:124061400-124066600	Weak transcription	Fetal Thymus	thymus

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