Variant report

Variant	rs36061398
Chromosome Location	chr3:42781714-42781715
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:42781201..42784093-chr3:42790186..42792951,2	K562	blood:
2	chr3:42777883..42779575-chr3:42780647..42782304,2	K562	blood:
3	chr3:42779798..42781927-chr3:42890891..42893467,2	K562	blood:

Variant related genes	Relation type
ENSG00000144648	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs12485678	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12486439	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12487055	0.95[EUR][1000 genomes]
rs12488174	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12490743	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12492886	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12493321	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12495805	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13061576	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs13064320	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13072026	0.96[EUR][1000 genomes]
rs13085272	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13090185	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13095730	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1871121	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2240860	0.96[EUR][1000 genomes]
rs2372111	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2372114	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs339681	0.80[EUR][1000 genomes]
rs339693	0.83[ASN][1000 genomes]
rs339695	0.83[ASN][1000 genomes]
rs339696	0.83[ASN][1000 genomes]
rs34025253	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34188562	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34336220	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs34482203	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34510173	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34648075	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34974363	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs35389123	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35488977	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs35647815	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35659560	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35697625	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35766391	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3912102	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3912103	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3916333	0.94[EUR][1000 genomes]
rs4488806	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55799024	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56232384	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56978598	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62246602	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62246607	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62246631	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs62250122	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66665035	0.86[ASN][1000 genomes]
rs6765740	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6779396	0.96[EUR][1000 genomes]
rs6799524	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7429327	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7617368	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs36061398	CCDC13	cis	Thyroid	GTEx
rs36061398	CCDC13-AS1	cis	Thyroid	GTEx

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42769600-42785600	Weak transcription	Stomach Smooth Muscle	stomach
2	chr3:42769800-42787600	Weak transcription	Gastric	stomach
3	chr3:42776800-42787000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr3:42778000-42811000	Weak transcription	Spleen	Spleen
5	chr3:42778200-42788000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:42778400-42786400	Weak transcription	Right Ventricle	heart
7	chr3:42780400-42782600	Enhancers	Brain Cingulate Gyrus	brain
8	chr3:42780600-42781800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr3:42780600-42781800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr3:42780600-42782000	Enhancers	Primary B cells from peripheral blood	blood
11	chr3:42780600-42782200	Enhancers	Brain Inferior Temporal Lobe	brain
12	chr3:42780600-42782400	Enhancers	Brain Angular Gyrus	brain
13	chr3:42780600-42782600	Enhancers	Brain Anterior Caudate	brain
14	chr3:42780600-42783600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
15	chr3:42780600-42783800	Enhancers	Brain Hippocampus Middle	brain
16	chr3:42780600-42783800	Enhancers	Brain Substantia Nigra	brain
17	chr3:42780800-42781800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr3:42780800-42783600	Enhancers	Psoas Muscle	Psoas
19	chr3:42780800-42783800	Enhancers	Fetal Muscle Leg	muscle
20	chr3:42781000-42782000	Enhancers	HepG2	liver
21	chr3:42781000-42788600	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr3:42781200-42782200	Weak transcription	Left Ventricle	heart
23	chr3:42781200-42782400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr3:42781200-42783800	Enhancers	Fetal Heart	heart
25	chr3:42781200-42784800	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr3:42781200-42787400	Weak transcription	Aorta	Aorta
27	chr3:42781200-42788600	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr3:42781400-42783600	Enhancers	Right Atrium	heart
29	chr3:42781600-42782000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
30	chr3:42781600-42783400	Weak transcription	HSMMtube	muscle
31	chr3:42781600-42787400	Weak transcription	Fetal Muscle Trunk	muscle

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