Variant report

Variant	rs13070345
Chromosome Location	chr3:42792260-42792261
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:42789944..42792627-chr3:42845601..42848096,2	K562	blood:
2	chr3:42694253..42696988-chr3:42790179..42793098,2	K562	blood:
3	chr3:42781201..42784093-chr3:42790186..42792951,2	K562	blood:
4	chr3:42791485..42794252-chr3:42803648..42805435,2	K562	blood:
5	chr3:42791198..42793006-chr3:42796472..42798021,2	K562	blood:
6	chr3:42787545..42791354-chr3:42791558..42794985,4	K562	blood:

Variant related genes	Relation type
ENSG00000114853	Chromatin interaction
ENSG00000144648	Chromatin interaction
ENSG00000230084	Chromatin interaction
ENSG00000181061	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10490794	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10865922	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11718476	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11922251	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11929390	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12054446	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12487729	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12491179	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12633707	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12635736	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12639142	0.87[CHB][hapmap]
rs2240859	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs339684	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs339731	0.86[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs34549959	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3846063	0.87[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap]
rs3895740	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3907218	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3912104	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3916334	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60706321	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6807878	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7639170	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7639483	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9830553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9839430	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[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
rs13070345	LRRC2	cis	cerebellum	SCAN
rs13070345	ZNF35	cis	cerebellum	SCAN
rs13070345	HHATL	cis	parietal	SCAN
rs13070345	HHATL	cis	cerebellum	SCAN

Chromatin state (count:47 , 50 per page) page: 1

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	chr3:42788200-42794400	Weak transcription	Stomach Mucosa	stomach
4	chr3:42788400-42797200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr3:42788600-42793400	Weak transcription	Fetal Brain Male	brain
6	chr3:42788600-42796000	Weak transcription	Adipose Nuclei	Adipose
7	chr3:42788600-42804200	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr3:42788800-42793000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr3:42788800-42794400	Weak transcription	Gastric	stomach
10	chr3:42788800-42799800	Weak transcription	Left Ventricle	heart
11	chr3:42789000-42792600	Weak transcription	Fetal Lung	lung
12	chr3:42789000-42795200	Weak transcription	Aorta	Aorta
13	chr3:42789000-42795600	Weak transcription	Fetal Brain Female	brain
14	chr3:42789400-42793000	Weak transcription	Lung	lung
15	chr3:42789800-42807600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr3:42790200-42793200	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr3:42790600-42793600	Enhancers	Placenta	Placenta
18	chr3:42791000-42804000	Weak transcription	Brain Angular Gyrus	brain
19	chr3:42791400-42795400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr3:42791400-42797200	Weak transcription	Fetal Heart	heart
21	chr3:42791600-42797400	Weak transcription	Rectal Smooth Muscle	rectum
22	chr3:42791600-42803000	Weak transcription	Colonic Mucosa	Colon
23	chr3:42791800-42792400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr3:42791800-42792800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr3:42791800-42793000	Weak transcription	Fetal Muscle Trunk	muscle
26	chr3:42791800-42793000	Weak transcription	Fetal Muscle Leg	muscle
27	chr3:42791800-42793000	Weak transcription	Fetal Stomach	stomach
28	chr3:42791800-42797000	Weak transcription	Colon Smooth Muscle	Colon
29	chr3:42791800-42797200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr3:42791800-42797200	Weak transcription	Brain Anterior Caudate	brain
31	chr3:42791800-42797800	Weak transcription	Pancreas	Pancrea
32	chr3:42791800-42804000	Weak transcription	Right Ventricle	heart
33	chr3:42791800-42807200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr3:42792000-42792800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr3:42792000-42793000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr3:42792000-42793000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr3:42792000-42793000	Weak transcription	Brain Cingulate Gyrus	brain
38	chr3:42792000-42793000	Weak transcription	Brain Hippocampus Middle	brain
39	chr3:42792000-42793000	Weak transcription	Brain Substantia Nigra	brain
40	chr3:42792000-42793000	Weak transcription	Right Atrium	heart
41	chr3:42792000-42793200	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr3:42792000-42795600	Weak transcription	HepG2	liver
43	chr3:42792000-42797200	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr3:42792000-42797200	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr3:42792000-42797200	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr3:42792000-42802800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr3:42792200-42792600	Weak transcription	Stomach Smooth Muscle	stomach

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