Variant report

Variant	rs12774597
Chromosome Location	chr10:116755682-116755683
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 109 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10160015	0.90[ASN][1000 genomes]
rs10444099	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1045657	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10490908	1.00[JPT][hapmap]
rs10510008	0.81[ASN][1000 genomes]
rs10885632	0.81[ASN][1000 genomes]
rs10885633	1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10885634	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10885636	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10885637	1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs10885638	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.95[ASN][1000 genomes]
rs10885639	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11196983	0.81[ASN][1000 genomes]
rs11196984	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11196989	0.81[ASN][1000 genomes]
rs11196991	0.95[ASN][1000 genomes]
rs11196996	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[ASN][1000 genomes]
rs11196999	1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[ASN][1000 genomes]
rs11197000	1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11197005	0.95[ASN][1000 genomes]
rs11197006	0.87[ASN][1000 genomes]
rs11197007	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11197010	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11197011	1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs11197012	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11197023	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12098332	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12246008	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12265048	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12269261	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12761122	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12764662	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];1.00[ASN][1000 genomes]
rs12772737	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12775180	1.00[JPT][hapmap]
rs12779231	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17092542	1.00[JPT][hapmap]
rs17092671	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17721283	1.00[JPT][hapmap]
rs17721905	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17722042	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17794346	1.00[JPT][hapmap]
rs17795104	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17795212	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1966384	1.00[JPT][hapmap]
rs2095379	0.95[ASN][1000 genomes]
rs2105001	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2420070	0.81[ASN][1000 genomes]
rs34170154	1.00[ASN][1000 genomes]
rs34200762	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34318200	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34434610	1.00[ASN][1000 genomes]
rs34453431	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34461950	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35501899	1.00[ASN][1000 genomes]
rs35811923	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3931556	1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs61869271	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs61869272	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61869274	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61869275	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6585302	0.81[ASN][1000 genomes]
rs6585306	0.95[ASN][1000 genomes]
rs6585308	0.84[CEU][hapmap]
rs6585309	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6585310	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6585311	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6585313	1.00[ASN][1000 genomes]
rs7071789	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7071812	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7072356	1.00[JPT][hapmap]
rs7074729	1.00[JPT][hapmap]
rs7075888	1.00[JPT][hapmap]
rs7079234	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7085964	0.90[ASN][1000 genomes]
rs7086663	0.84[CEU][hapmap]
rs7093282	0.87[ASN][1000 genomes]
rs7093330	1.00[ASN][1000 genomes]
rs7094072	1.00[JPT][hapmap]
rs7097580	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7099565	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7099590	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7099779	0.95[ASN][1000 genomes]
rs7100026	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7100159	0.95[ASN][1000 genomes]
rs7100894	0.81[ASN][1000 genomes]
rs72836518	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs749649	1.00[JPT][hapmap]
rs7895551	1.00[JPT][hapmap]
rs7898249	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7904605	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7908069	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7908464	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7909566	1.00[JPT][hapmap]
rs7909657	1.00[JPT][hapmap]
rs7917523	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs7923295	1.00[JPT][hapmap]
rs881192	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs968848	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs968849	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949138	chr10:116311531-116874477	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1038050	chr10:116315109-116895719	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv533027	chr10:116344641-116856352	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	esv3435429	chr10:116394152-117006347	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv831996	chr10:116601552-116772968	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv1039002	chr10:116643095-116879483	Active TSS Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	esv2761634	chr10:116643095-116879495	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv1045654	chr10:116654574-116879483	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv1043242	chr10:116655057-116883386	Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
10	nsv831997	chr10:116689552-116855698	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12774597	ATRNL1	cis	Muscle Skeletal	GTEx
rs12774597	TRUB1	Cis_1M	lymphoblastoid	RTeQTL
rs12774597	NHLRC2	cis	cerebellum	SCAN
rs12774597	TRUB1	cis	parietal	SCAN
rs12774597	TRUB1	cis	cerebellum	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:116698800-116763600	Weak transcription	Esophagus	oesophagus
2	chr10:116723000-116760800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr10:116731000-116761200	Weak transcription	Pancreas	Pancrea
4	chr10:116737400-116759800	Weak transcription	Hela-S3	cervix
5	chr10:116742200-116761600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr10:116742600-116763400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr10:116742600-116763400	Weak transcription	Lung	lung
8	chr10:116744200-116756400	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr10:116744200-116758600	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr10:116744400-116756800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr10:116744600-116756600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr10:116744600-116756800	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr10:116745000-116759200	Weak transcription	Left Ventricle	heart
14	chr10:116745000-116761200	Weak transcription	Adipose Nuclei	Adipose
15	chr10:116745600-116760400	Weak transcription	Liver	Liver
16	chr10:116745800-116761800	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr10:116746000-116760800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr10:116746000-116761000	Weak transcription	Primary B cells from cord blood	blood
19	chr10:116746800-116757800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr10:116746800-116761000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr10:116747200-116761200	Weak transcription	Dnd41	blood
22	chr10:116747800-116760400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr10:116748200-116761000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr10:116748400-116761000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr10:116748400-116761000	Weak transcription	Aorta	Aorta
26	chr10:116748400-116761200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr10:116749000-116761200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr10:116750400-116760800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr10:116751000-116757200	Weak transcription	Brain Hippocampus Middle	brain
30	chr10:116752200-116760800	Weak transcription	Brain Angular Gyrus	brain
31	chr10:116752400-116756800	Weak transcription	Ovary	ovary
32	chr10:116752800-116761400	Weak transcription	Placenta	Placenta
33	chr10:116752800-116763600	Weak transcription	Spleen	Spleen
34	chr10:116754200-116756000	Enhancers	Fetal Brain Male	brain
35	chr10:116754400-116756000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr10:116754400-116761400	Weak transcription	Primary T cells from cord blood	blood
37	chr10:116755000-116757200	Enhancers	Osteobl	bone
38	chr10:116755200-116755800	Flanking Active TSS	NH-A	brain
39	chr10:116755200-116756000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr10:116755200-116756000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr10:116755200-116756200	Enhancers	HSMM	muscle
42	chr10:116755200-116756800	Enhancers	Muscle Satellite Cultured Cells	--
43	chr10:116755200-116757200	Enhancers	NHDF-Ad	bronchial
44	chr10:116755200-116757800	Enhancers	Brain Germinal Matrix	brain
45	chr10:116755200-116757800	Enhancers	HSMMtube	muscle
46	chr10:116755200-116758800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr10:116755400-116755800	Active TSS	Fetal Brain Female	brain
48	chr10:116755400-116756200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr10:116755600-116756000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr10:116755600-116756000	Flanking Active TSS	NHLF	lung

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