Variant report

Variant	rs12220941
Chromosome Location	chr10:96275039-96275040
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10882476	0.84[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.80[EUR][1000 genomes]
rs11187933	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11187953	0.91[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11187968	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11187969	0.81[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap]
rs11187971	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11187974	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11187994	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11188000	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11188001	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11527882	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11528075	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2265045	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2764379	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs495896	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7093613	0.82[ASW][hapmap];0.84[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.80[EUR][1000 genomes]
rs7901625	0.90[CEU][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2761616	chr10:95966768-96303701	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv497859	chr10:96058024-97027747	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	esv1819509	chr10:96064300-96361776	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv1053747	chr10:96211618-96366396	Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12220941	SCARNA3	trans	lymphoblastoid	seeQTL

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:96211600-96292200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr10:96219800-96283400	Weak transcription	Lung	lung
3	chr10:96223200-96293600	Weak transcription	NHDF-Ad	bronchial
4	chr10:96244000-96282600	Weak transcription	Duodenum Mucosa	Duodenum
5	chr10:96244400-96283600	Weak transcription	Pancreas	Pancrea
6	chr10:96244400-96304600	Weak transcription	Aorta	Aorta
7	chr10:96249200-96286200	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr10:96249400-96288600	Weak transcription	Gastric	stomach
9	chr10:96250400-96281000	Weak transcription	Brain Cingulate Gyrus	brain
10	chr10:96250800-96281000	Weak transcription	Brain Angular Gyrus	brain
11	chr10:96250800-96294000	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr10:96250800-96297400	Weak transcription	Small Intestine	intestine
13	chr10:96256200-96283600	Weak transcription	Osteobl	bone
14	chr10:96256800-96283800	Weak transcription	Liver	Liver
15	chr10:96257000-96293400	Weak transcription	HepG2	liver
16	chr10:96261000-96304400	Weak transcription	NH-A	brain
17	chr10:96264200-96296800	Weak transcription	Brain Germinal Matrix	brain
18	chr10:96266000-96304600	Weak transcription	Fetal Kidney	kidney
19	chr10:96267400-96303800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr10:96267800-96280800	Weak transcription	Brain Anterior Caudate	brain
21	chr10:96268200-96283400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr10:96268400-96304400	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr10:96268600-96279200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr10:96268800-96285800	Weak transcription	Fetal Lung	lung
25	chr10:96268800-96297200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr10:96268800-96304400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr10:96269200-96283600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr10:96269400-96283800	Weak transcription	Ovary	ovary
29	chr10:96269400-96285800	Weak transcription	Colon Smooth Muscle	Colon
30	chr10:96269600-96292000	Weak transcription	Brain Hippocampus Middle	brain
31	chr10:96270200-96285000	Weak transcription	Right Ventricle	heart
32	chr10:96270200-96304200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr10:96270400-96278800	Strong transcription	Fetal Stomach	stomach
34	chr10:96270400-96281000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr10:96270600-96278600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr10:96270800-96285600	Weak transcription	Esophagus	oesophagus
37	chr10:96271800-96294000	Weak transcription	Psoas Muscle	Psoas
38	chr10:96271800-96304000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr10:96272000-96276800	Weak transcription	Left Ventricle	heart
40	chr10:96272000-96283600	Weak transcription	Fetal Muscle Leg	muscle
41	chr10:96272000-96283800	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr10:96272000-96283800	Weak transcription	Placenta	Placenta
43	chr10:96272000-96294000	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr10:96272000-96304600	Weak transcription	HSMMtube	muscle
45	chr10:96272200-96281600	Weak transcription	Stomach Smooth Muscle	stomach
46	chr10:96272200-96295800	Weak transcription	Primary hematopoietic stem cells	blood
47	chr10:96272400-96283800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr10:96272400-96283800	Weak transcription	Brain Substantia Nigra	brain
49	chr10:96272400-96293000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr10:96272600-96279400	Weak transcription	Rectal Mucosa Donor 31	rectum

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