Variant report

Variant	rs786449
Chromosome Location	chr12:124071728-124071729
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 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

No data

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

No.	Distal block	Cell Line	Cell type
1	chr12:123892437..123894843-chr12:124070809..124073314,2	MCF-7	breast:
2	chr12:124067302..124072457-chr12:124084684..124088760,8	K562	blood:
3	chr12:124068831..124072178-chr12:124116882..124120107,5	K562	blood:
4	chr12:124067363..124072745-chr12:124084857..124088217,7	K562	blood:
5	chr12:124015697..124018727-chr12:124070609..124072770,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000247373	TF binding region
ENSG00000188026	Chromatin interaction
ENSG00000111361	Chromatin interaction
ENSG00000111364	Chromatin interaction
ENSG00000111358	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10846531	0.84[ASN][1000 genomes]
rs10846535	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11057307	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11615300	0.80[EUR][1000 genomes]
rs1515814	0.90[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	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4040225	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4456350	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6488883	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6551	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7134896	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7302183	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7313628	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs786422	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786423	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786425	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786441	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs786443	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786444	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786445	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786447	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786448	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786452	0.90[ASN][1000 genomes]
rs7966882	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7972413	0.87[AMR][1000 genomes];0.85[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
rs786449	TCTN2	cis	Adipose Subcutaneous	GTEx
rs786449	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	chr12:124070000-124071800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
2	chr12:124070000-124073000	Weak transcription	Lung	lung
3	chr12:124070000-124073200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:124070000-124073200	Weak transcription	Esophagus	oesophagus
5	chr12:124070000-124085800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr12:124070200-124072000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr12:124070200-124073200	Weak transcription	Aorta	Aorta
8	chr12:124070200-124073400	Weak transcription	Stomach Mucosa	stomach
9	chr12:124070400-124071800	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr12:124070400-124071800	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr12:124070400-124072000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr12:124070400-124072200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr12:124070400-124072400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr12:124070400-124072400	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr12:124070400-124072400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr12:124070400-124072600	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr12:124070400-124072600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr12:124070400-124072600	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr12:124070400-124072600	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr12:124070400-124073200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr12:124070400-124073200	Weak transcription	Gastric	stomach
22	chr12:124070400-124073200	Weak transcription	Pancreas	Pancrea
23	chr12:124070400-124073800	Genic enhancers	Stomach Smooth Muscle	stomach
24	chr12:124070400-124076400	Weak transcription	Ovary	ovary
25	chr12:124070400-124076600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr12:124070600-124071800	Weak transcription	Brain Cingulate Gyrus	brain
27	chr12:124070600-124071800	Weak transcription	Psoas Muscle	Psoas
28	chr12:124070600-124072000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr12:124070600-124072000	Weak transcription	Rectal Smooth Muscle	rectum
30	chr12:124070600-124072200	Enhancers	HSMMtube	muscle
31	chr12:124070600-124072400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr12:124070600-124072600	Strong transcription	Cortex derived primary cultured neurospheres	brain
33	chr12:124070600-124072600	Weak transcription	Colonic Mucosa	Colon
34	chr12:124070600-124072600	Weak transcription	Right Ventricle	heart
35	chr12:124070600-124073000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr12:124070600-124073400	Weak transcription	Right Atrium	heart
37	chr12:124070600-124073400	Genic enhancers	NHEK	skin
38	chr12:124070600-124082200	Strong transcription	Fetal Muscle Leg	muscle
39	chr12:124070600-124084400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr12:124070800-124071800	Weak transcription	Colon Smooth Muscle	Colon
41	chr12:124070800-124071800	Strong transcription	K562	blood
42	chr12:124070800-124072000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr12:124070800-124072000	Weak transcription	Brain Hippocampus Middle	brain
44	chr12:124070800-124072000	Weak transcription	Fetal Brain Female	brain
45	chr12:124070800-124072000	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr12:124070800-124072400	Weak transcription	Primary B cells from cord blood	blood
47	chr12:124070800-124072400	Weak transcription	Fetal Intestine Small	intestine
48	chr12:124070800-124072400	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr12:124070800-124074200	Genic enhancers	Dnd41	blood
50	chr12:124070800-124074600	Genic enhancers	Primary T helper cells PMA-I stimulated	--

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