Variant report

Variant	rs12813346
Chromosome Location	chr12:124201114-124201115
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:124197317..124199862-chr12:124200055..124203034,3	K562	blood:
2	chr12:124192727..124194757-chr12:124200394..124202441,2	K562	blood:

Variant related genes	Relation type
ENSG00000255839	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10846535	0.85[EUR][1000 genomes]
rs10846540	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10846541	0.83[ASN][1000 genomes]
rs10846546	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11057307	0.80[EUR][1000 genomes]
rs11057320	0.91[EUR][1000 genomes]
rs11609591	0.81[EUR][1000 genomes]
rs11614659	0.80[EUR][1000 genomes]
rs11829958	0.81[EUR][1000 genomes]
rs12819746	0.82[EUR][1000 genomes]
rs12821219	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12825800	0.82[EUR][1000 genomes]
rs12828633	0.81[EUR][1000 genomes]
rs1515814	0.81[EUR][1000 genomes]
rs1969272	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2222061	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2250026	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35114195	0.81[EUR][1000 genomes]
rs35158437	0.81[EUR][1000 genomes]
rs3748269	0.80[EUR][1000 genomes]
rs6488883	0.80[EUR][1000 genomes]
rs6488897	0.82[EUR][1000 genomes]
rs66647364	0.81[EUR][1000 genomes]
rs7134074	0.81[EUR][1000 genomes]
rs7134896	0.80[EUR][1000 genomes]
rs7135624	0.90[EUR][1000 genomes]
rs7137946	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7138503	0.80[EUR][1000 genomes]
rs7139193	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7297576	0.81[EUR][1000 genomes]
rs7298831	0.81[EUR][1000 genomes]
rs7301907	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7302183	0.80[EUR][1000 genomes]
rs7302449	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7305701	0.81[EUR][1000 genomes]
rs7306549	0.81[EUR][1000 genomes]
rs7308862	0.81[EUR][1000 genomes]
rs7313032	0.81[EUR][1000 genomes]
rs7313140	0.81[EUR][1000 genomes]
rs7313261	0.81[EUR][1000 genomes]
rs7313628	0.81[EUR][1000 genomes]
rs7958693	0.81[EUR][1000 genomes]
rs7960951	0.80[EUR][1000 genomes]
rs7964443	0.81[EUR][1000 genomes]
rs7966867	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7966882	0.81[EUR][1000 genomes]
rs7974279	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv832534	chr12:124157605-124234611	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12813346	TCTN2	cis	Artery Tibial	GTEx
rs12813346	TCTN2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124197600-124234400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:124197800-124202600	Weak transcription	Fetal Muscle Trunk	muscle
3	chr12:124198200-124203800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr12:124198200-124204400	Weak transcription	Aorta	Aorta
5	chr12:124198200-124207000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:124198200-124207200	Weak transcription	Ovary	ovary
7	chr12:124198400-124203600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr12:124198400-124203800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr12:124198400-124203800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr12:124198400-124204400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr12:124198400-124204400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr12:124198400-124210600	Weak transcription	NH-A	brain
13	chr12:124198600-124202200	Weak transcription	Fetal Stomach	stomach
14	chr12:124198600-124203400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr12:124198600-124203800	Weak transcription	HUVEC	blood vessel
16	chr12:124198600-124204000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr12:124198600-124204000	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr12:124198600-124205000	Weak transcription	Stomach Smooth Muscle	stomach
19	chr12:124198600-124205600	Weak transcription	HSMM	muscle
20	chr12:124198600-124205800	Weak transcription	HMEC	breast
21	chr12:124198600-124206800	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr12:124198600-124207200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr12:124198600-124212400	Weak transcription	NHLF	lung
24	chr12:124198800-124202600	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr12:124198800-124203400	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr12:124198800-124203600	Weak transcription	Brain Angular Gyrus	brain
27	chr12:124198800-124203600	Weak transcription	Brain Anterior Caudate	brain
28	chr12:124198800-124203800	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr12:124198800-124204200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr12:124198800-124204200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr12:124198800-124204200	Weak transcription	Brain Hippocampus Middle	brain
32	chr12:124198800-124204400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr12:124198800-124204400	Weak transcription	Placenta	Placenta
34	chr12:124198800-124205000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr12:124198800-124205800	Weak transcription	A549	lung
36	chr12:124198800-124205800	Weak transcription	Osteobl	bone
37	chr12:124198800-124210800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr12:124198800-124223600	Weak transcription	Right Atrium	heart
39	chr12:124199000-124201400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr12:124199000-124201400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr12:124199000-124203600	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr12:124199000-124203600	Weak transcription	Fetal Muscle Leg	muscle
43	chr12:124199000-124203800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr12:124199000-124203800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr12:124199000-124203800	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr12:124199000-124203800	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr12:124199000-124204000	Weak transcription	Right Ventricle	heart
48	chr12:124199000-124204200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr12:124199000-124204200	Weak transcription	Left Ventricle	heart
50	chr12:124199000-124204200	Weak transcription	Lung	lung

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