Variant report

Variant	rs7617368
Chromosome Location	chr3:42774148-42774149
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KBTBD5-2	chr3:42774067-42774150	ENSG00000173811.6
2	lnc-KBTBD5-2	chr3:42774069-42774150	ENSG00000173811.6

Extended variants
information (count: 56 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs12485678	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12486439	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12487055	0.93[CEU][hapmap];0.97[EUR][1000 genomes]
rs12488174	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12490743	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12492886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12493321	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12495805	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13061576	0.87[CEU][hapmap];0.81[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[AMR][1000 genomes]
rs13064320	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13072026	0.93[CEU][hapmap];0.80[GIH][hapmap];0.93[TSI][hapmap];0.97[EUR][1000 genomes]
rs13085272	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13090185	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13095730	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17317763	0.85[CEU][hapmap]
rs1871121	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2240860	0.93[CEU][hapmap];0.93[TSI][hapmap];0.97[EUR][1000 genomes]
rs2290972	0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2372111	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2372114	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs339681	0.82[CEU][hapmap]
rs339693	0.81[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs339695	0.86[ASN][1000 genomes]
rs339696	0.86[ASN][1000 genomes]
rs34025253	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34188562	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34336220	0.83[AMR][1000 genomes]
rs34482203	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34510173	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34648075	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs34974363	0.83[AMR][1000 genomes]
rs35389123	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35488977	0.83[AMR][1000 genomes]
rs35647815	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs35659560	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35697625	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35766391	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36061398	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3912102	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3912103	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3916333	0.96[EUR][1000 genomes]
rs4488806	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55799024	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56232384	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56978598	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62246602	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62246607	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62246631	0.83[AMR][1000 genomes]
rs62250122	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66665035	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6765740	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6779396	0.97[EUR][1000 genomes]
rs6799524	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7429327	0.80[AMR][1000 genomes];0.92[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7617368	CCDC13	cis	Whole Blood	GTEx
rs7617368	CCDC13-AS1	cis	Thyroid	GTEx
rs7617368	CCDC13	cis	Thyroid	GTEx

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42763600-42774800	Enhancers	Brain Angular Gyrus	brain
2	chr3:42767800-42774400	Enhancers	Brain Cingulate Gyrus	brain
3	chr3:42768600-42776000	Enhancers	Skeletal Muscle Female	skeletal muscle
4	chr3:42769000-42774200	Enhancers	Brain Inferior Temporal Lobe	brain
5	chr3:42769000-42774800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
6	chr3:42769000-42775000	Enhancers	Skeletal Muscle Male	skeletal muscle
7	chr3:42769600-42785600	Weak transcription	Stomach Smooth Muscle	stomach
8	chr3:42769800-42774200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr3:42769800-42787600	Weak transcription	Gastric	stomach
10	chr3:42770200-42774200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr3:42770600-42775600	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr3:42771000-42774200	Enhancers	Right Atrium	heart
13	chr3:42771200-42775800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr3:42772600-42777600	Weak transcription	Left Ventricle	heart
15	chr3:42772600-42778200	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr3:42773000-42774600	Enhancers	Pancreas	Pancrea
17	chr3:42773000-42778400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr3:42773200-42774400	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr3:42773200-42776800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr3:42773400-42774400	Weak transcription	Fetal Heart	heart
21	chr3:42773400-42774600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr3:42773600-42774600	Flanking Active TSS	Brain Anterior Caudate	brain
23	chr3:42773600-42775200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr3:42773600-42775600	Flanking Active TSS	Brain Hippocampus Middle	brain
25	chr3:42773600-42776400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr3:42773800-42774600	Enhancers	Psoas Muscle	Psoas
27	chr3:42773800-42775400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr3:42773800-42775400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr3:42773800-42775600	Enhancers	Brain Germinal Matrix	brain
30	chr3:42773800-42776600	Enhancers	H1 Cell Line	embryonic stem cell
31	chr3:42773800-42776800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr3:42773800-42777600	Weak transcription	Fetal Muscle Leg	muscle
33	chr3:42774000-42774200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr3:42774000-42774800	Flanking Active TSS	HepG2	liver
35	chr3:42774000-42775200	Flanking Active TSS	Brain Substantia Nigra	brain
36	chr3:42774000-42775400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:42774000-42776400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr3:42774000-42776400	Enhancers	iPS-18 Cell Line	embryonic stem cell
39	chr3:42774000-42777400	Weak transcription	Right Ventricle	heart

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