Variant report

Variant	rs786425
Chromosome Location	chr12:124085502-124085503
allele	A/G
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:16)
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	chr12:124085359-124085832	SK-N-MC	brain:	n/a	n/a

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:123942486..123944135-chr12:124085124..124087552,2	MCF-7	breast:
2	chr12:124067363..124072745-chr12:124084857..124088217,7	K562	blood:
3	chr12:124084988..124092992-chr12:124114351..124121638,14	K562	blood:
4	chr12:123716942..123720349-chr12:124084108..124086499,3	K562	blood:
5	chr12:124017444..124019100-chr12:124084646..124086674,2	MCF-7	breast:
6	chr12:124084914..124087862-chr12:124122413..124125179,2	K562	blood:
7	chr12:124084893..124086565-chr12:124117453..124119818,2	K562	blood:
8	chr12:123941486..123944276-chr12:124085171..124087519,2	K562	blood:
9	chr12:123872056..123874942-chr12:124085224..124088307,3	MCF-7	breast:
10	chr12:123755058..123757440-chr12:124084744..124087456,3	K562	blood:
11	chr12:124085496..124088026-chr12:124116630..124119648,4	MCF-7	breast:
12	chr12:124067302..124072457-chr12:124084684..124088760,8	K562	blood:
13	chr12:124085449..124088387-chr12:124115552..124120028,6	MCF-7	breast:
14	chr12:124084644..124087346-chr12:124096148..124098451,3	K562	blood:
15	chr12:124084509..124086598-chr12:124112180..124115159,2	K562	blood:
16	chr12:123847169..123849970-chr12:124085128..124088523,3	K562	blood:

No data

Variant related genes	Relation type
DDX55	TF binding region
ENSG00000111358	Chromatin interaction
ENSG00000111364	Chromatin interaction
ENSG00000111361	Chromatin interaction
ENSG00000183955	Chromatin interaction
ENSG00000051825	Chromatin interaction
ENSG00000256092	Chromatin interaction
ENSG00000184209	Chromatin interaction
ENSG00000111328	Chromatin interaction
ENSG00000130921	Chromatin interaction
ENSG00000188026	Chromatin interaction
ENSG00000247373	Chromatin interaction
ENSG00000086598	Chromatin interaction
ENSG00000139697	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10846531	0.84[ASN][1000 genomes]
rs10846535	0.86[EUR][1000 genomes]
rs11057307	0.83[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	0.80[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	0.88[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4040225	0.83[CEU][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4456350	0.88[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6488883	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6551	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7134896	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7135624	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7137946	0.81[CEU][hapmap]
rs7139193	0.81[CEU][hapmap]
rs7302183	0.87[CEU][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7313628	0.85[CEU][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs786422	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786423	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786441	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs786443	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786444	0.88[CEU][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786445	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786447	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786448	0.88[CEU][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786449	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786452	0.90[ASN][1000 genomes]
rs7966867	0.81[CEU][hapmap]
rs7966882	0.83[EUR][1000 genomes]
rs7972413	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs884892	0.84[ASN][1000 genomes]
rs908373	0.81[CEU][hapmap];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

Variant related diseases (count:1)

Disease	PMID	Source
Pubertal anthropometrics	23449627	GWAS catalog

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs786425	TCTN2	cis	Artery Tibial	GTEx
rs786425	DDX55	cis	Artery Aorta	GTEx
rs786425	TCTN2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124070000-124085800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:124072200-124085800	Weak transcription	Small Intestine	intestine
3	chr12:124074200-124086000	Weak transcription	Fetal Heart	heart
4	chr12:124075200-124085600	Weak transcription	Right Ventricle	heart
5	chr12:124075200-124085800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr12:124075200-124086000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:124075200-124086000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr12:124076800-124085600	Weak transcription	Pancreas	Pancrea
9	chr12:124077000-124085600	Weak transcription	Spleen	Spleen
10	chr12:124077000-124086200	Weak transcription	Aorta	Aorta
11	chr12:124077400-124086000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr12:124077400-124086000	Weak transcription	Fetal Brain Male	brain
13	chr12:124078400-124085600	Weak transcription	Esophagus	oesophagus
14	chr12:124079400-124085600	Weak transcription	Fetal Stomach	stomach
15	chr12:124079400-124085600	Weak transcription	Lung	lung
16	chr12:124080000-124085800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr12:124080600-124086000	Weak transcription	Ovary	ovary
18	chr12:124081800-124085600	Weak transcription	Brain Cingulate Gyrus	brain
19	chr12:124082000-124085600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr12:124082000-124086000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr12:124082200-124085600	Weak transcription	Brain Angular Gyrus	brain
22	chr12:124082200-124085600	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr12:124082200-124085600	Weak transcription	Colon Smooth Muscle	Colon
24	chr12:124082200-124085600	Weak transcription	Fetal Muscle Leg	muscle
25	chr12:124082200-124085600	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr12:124082200-124085800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr12:124082200-124086000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr12:124082400-124085600	Weak transcription	Psoas Muscle	Psoas
29	chr12:124082400-124085800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr12:124082800-124085600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr12:124082800-124085600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr12:124082800-124086000	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr12:124083000-124085600	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr12:124083200-124085600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr12:124083400-124085600	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr12:124083400-124085600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr12:124083400-124085600	Weak transcription	Adipose Nuclei	Adipose
38	chr12:124083400-124085600	Weak transcription	Fetal Kidney	kidney
39	chr12:124083400-124085600	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr12:124083400-124085600	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr12:124083400-124085600	Weak transcription	HMEC	breast
42	chr12:124083400-124085600	Weak transcription	HSMMtube	muscle
43	chr12:124083400-124085600	Weak transcription	HUVEC	blood vessel
44	chr12:124083400-124085600	Weak transcription	NHDF-Ad	bronchial
45	chr12:124083400-124086000	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr12:124083400-124086000	Weak transcription	NH-A	brain
47	chr12:124083600-124085600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr12:124083600-124085600	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr12:124083600-124085600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr12:124083600-124085600	Weak transcription	Primary monocytes fromperipheralblood	blood

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