Variant report

Variant	rs7429327
Chromosome Location	chr3:42816871-42816872
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUND	chr3:42816801-42816969	HepG2	liver:	n/a	chr3:42816857-42816868

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:42816806..42819669-chr3:42844810..42846468,2	K562	blood:

Variant related genes	Relation type
CCDC13	TF binding region
ENSG00000181061	Chromatin interaction
ENSG00000144648	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs12485678	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12486439	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12488174	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12490743	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12492886	0.92[ASN][1000 genomes]
rs12493321	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12495805	0.92[ASN][1000 genomes]
rs13061576	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13064320	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13085272	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs13090185	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13095730	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17317763	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1871121	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2372111	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2372114	0.95[ASN][1000 genomes]
rs339681	0.95[EUR][1000 genomes]
rs339693	0.84[ASN][1000 genomes]
rs339695	0.84[ASN][1000 genomes]
rs339696	0.84[ASN][1000 genomes]
rs34025253	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34188562	0.92[ASN][1000 genomes]
rs34336220	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34482203	0.95[ASN][1000 genomes]
rs34510173	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34648075	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34974363	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35389123	0.92[ASN][1000 genomes]
rs35488977	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35647815	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35697625	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35766391	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35919797	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs36061398	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3912102	0.92[ASN][1000 genomes]
rs3912103	0.92[ASN][1000 genomes]
rs4488806	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55799024	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs56232384	0.92[ASN][1000 genomes]
rs56978598	0.92[ASN][1000 genomes]
rs62246602	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs62246607	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62246631	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62246641	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62250122	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs66665035	0.84[ASN][1000 genomes]
rs6765740	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6799524	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7617368	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013578	chr3:42747858-42817321	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv999713	chr3:42749022-42817321	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	esv1846968	chr3:42787469-42832979	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7429327	CCDC13	cis	Thyroid	GTEx
rs7429327	CCDC13-AS1	cis	Thyroid	GTEx

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42813000-42821400	Weak transcription	Dnd41	blood
2	chr3:42813000-42821800	Weak transcription	HepG2	liver
3	chr3:42814600-42822200	Weak transcription	Fetal Heart	heart
4	chr3:42814800-42819200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr3:42814800-42823800	Weak transcription	Lung	lung
6	chr3:42814800-42824800	Weak transcription	Gastric	stomach
7	chr3:42814800-42840800	Weak transcription	Spleen	Spleen
8	chr3:42815000-42820200	Weak transcription	Pancreas	Pancrea
9	chr3:42815000-42821400	Weak transcription	Esophagus	oesophagus
10	chr3:42815000-42823200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr3:42815000-42824800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr3:42815000-42834800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr3:42815200-42817600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:42815200-42817600	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr3:42815200-42818400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr3:42815200-42819200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr3:42815200-42819400	Weak transcription	Right Atrium	heart
18	chr3:42815200-42819800	Weak transcription	HSMMtube	muscle
19	chr3:42815200-42820000	Weak transcription	Liver	Liver
20	chr3:42815200-42820000	Weak transcription	Fetal Stomach	stomach
21	chr3:42815200-42821000	Weak transcription	NHEK	skin
22	chr3:42815200-42821200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr3:42815200-42821400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr3:42815200-42821600	Weak transcription	Stomach Mucosa	stomach
25	chr3:42815200-42821600	Weak transcription	K562	blood
26	chr3:42815200-42821800	Weak transcription	Fetal Kidney	kidney
27	chr3:42815200-42822200	Weak transcription	Primary B cells from peripheral blood	blood
28	chr3:42815200-42822200	Weak transcription	Brain Angular Gyrus	brain
29	chr3:42815200-42822600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr3:42815200-42822600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr3:42815200-42822600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr3:42815200-42822800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr3:42815200-42823000	Weak transcription	Colonic Mucosa	Colon
34	chr3:42815200-42823600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr3:42815200-42823600	Weak transcription	Placenta	Placenta
36	chr3:42815200-42823800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr3:42815200-42823800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr3:42815200-42823800	Weak transcription	Fetal Brain Female	brain
39	chr3:42815200-42823800	Weak transcription	Left Ventricle	heart
40	chr3:42815200-42823800	Weak transcription	GM12878-XiMat	blood
41	chr3:42815200-42823800	Weak transcription	HMEC	breast
42	chr3:42815200-42824000	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr3:42815200-42824000	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr3:42815200-42824000	Weak transcription	HSMM	muscle
45	chr3:42815200-42824200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr3:42815200-42824400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr3:42815200-42824400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr3:42815200-42824600	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr3:42815200-42824600	Weak transcription	Duodenum Mucosa	Duodenum
50	chr3:42815200-42824600	Weak transcription	NH-A	brain

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