Variant report

Variant	rs13095730
Chromosome Location	chr3:42789316-42789317
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:42787545..42791354-chr3:42791558..42794985,4	K562	blood:

Extended variants
information (count: 57 )
Associated
traits (count: 4 )

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];0.93[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12486439	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12487055	0.93[CEU][hapmap];0.94[EUR][1000 genomes]
rs12488174	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12490743	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12492886	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12493321	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12495805	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13061576	0.87[CEU][hapmap];0.81[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs13064320	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13072026	0.93[CEU][hapmap];0.81[GIH][hapmap];0.90[TSI][hapmap];0.95[EUR][1000 genomes]
rs13085272	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13090185	0.87[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.83[MEX][hapmap];0.93[YRI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17317763	0.85[CEU][hapmap]
rs1871121	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2240860	0.93[CEU][hapmap];0.90[TSI][hapmap];0.95[EUR][1000 genomes]
rs2290972	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2372111	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2372114	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs339681	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs339693	0.81[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs339695	0.83[ASN][1000 genomes]
rs339696	0.83[ASN][1000 genomes]
rs34025253	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34188562	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34336220	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs34482203	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34510173	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34648075	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34974363	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs35389123	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35488977	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs35647815	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35659560	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35697625	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35766391	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36061398	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3912102	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3912103	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3916333	0.93[EUR][1000 genomes]
rs4488806	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55799024	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56232384	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56978598	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62246602	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62246607	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62246631	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs62250122	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66665035	0.86[ASN][1000 genomes]
rs6765740	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6779396	0.95[EUR][1000 genomes]
rs6799524	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7429327	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7617368	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]

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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13095730	CCDC13	cis	Whole Blood	GTEx
rs13095730	CCDC13-AS1	cis	Whole Blood	GTEx
rs13095730	CCDC13	cis	Thyroid	GTEx
rs13095730	CCDC13-AS1	cis	Thyroid	GTEx

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42778000-42811000	Weak transcription	Spleen	Spleen
2	chr3:42781800-42802800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr3:42785200-42790200	Enhancers	Brain Anterior Caudate	brain
4	chr3:42785200-42792000	Enhancers	Brain Inferior Temporal Lobe	brain
5	chr3:42785200-42792000	Enhancers	Brain Substantia Nigra	brain
6	chr3:42785400-42790200	Enhancers	Brain Hippocampus Middle	brain
7	chr3:42785400-42792000	Enhancers	Brain Cingulate Gyrus	brain
8	chr3:42785600-42790200	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr3:42785600-42791600	Enhancers	Rectal Smooth Muscle	rectum
10	chr3:42785600-42791800	Enhancers	Primary T cells fromperipheralblood	blood
11	chr3:42785800-42791800	Enhancers	Fetal Muscle Leg	muscle
12	chr3:42786400-42789400	Enhancers	Placenta	Placenta
13	chr3:42786400-42790200	Enhancers	Fetal Stomach	stomach
14	chr3:42786600-42790000	Enhancers	Duodenum Smooth Muscle	Duodenum
15	chr3:42786600-42790400	Enhancers	Brain Angular Gyrus	brain
16	chr3:42787200-42790000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr3:42787400-42789400	Enhancers	Lung	lung
18	chr3:42787400-42790000	Enhancers	Esophagus	oesophagus
19	chr3:42787400-42790800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr3:42787400-42791800	Enhancers	Fetal Muscle Trunk	muscle
21	chr3:42787600-42789800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr3:42787800-42790000	Enhancers	Pancreas	Pancrea
23	chr3:42787800-42790200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
24	chr3:42787800-42790800	Enhancers	Primary T helper cells fromperipheralblood	blood
25	chr3:42787800-42791200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr3:42788000-42792000	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr3:42788200-42790200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr3:42788200-42790200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr3:42788200-42790800	Enhancers	Primary T helper naive cells from peripheral blood	blood
30	chr3:42788200-42791000	Weak transcription	Fetal Heart	heart
31	chr3:42788200-42791800	Enhancers	Colon Smooth Muscle	Colon
32	chr3:42788200-42794400	Weak transcription	Stomach Mucosa	stomach
33	chr3:42788400-42789600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr3:42788400-42789800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
35	chr3:42788400-42797200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr3:42788600-42790000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr3:42788600-42790200	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr3:42788600-42790200	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr3:42788600-42790600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr3:42788600-42790800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr3:42788600-42790800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr3:42788600-42791000	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr3:42788600-42791000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr3:42788600-42793400	Weak transcription	Fetal Brain Male	brain
45	chr3:42788600-42796000	Weak transcription	Adipose Nuclei	Adipose
46	chr3:42788600-42804200	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr3:42788800-42789600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
48	chr3:42788800-42789600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
49	chr3:42788800-42789600	Enhancers	HMEC	breast
50	chr3:42788800-42789800	Enhancers	NHEK	skin

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