Variant report

Variant	rs1476105
Chromosome Location	chr7:69562563-69562564
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 117 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10235860	0.81[EUR][1000 genomes]
rs10268235	0.82[EUR][1000 genomes]
rs10270616	0.80[EUR][1000 genomes]
rs10279392	0.81[EUR][1000 genomes]
rs10499813	0.88[AFR][1000 genomes]
rs12112758	0.92[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs12113555	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12667561	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12669794	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12673575	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12698826	0.92[ASN][1000 genomes]
rs12698835	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12698838	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12698841	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12698842	0.81[EUR][1000 genomes]
rs12698843	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12698846	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12698847	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12698849	0.81[EUR][1000 genomes]
rs12698850	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12698851	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12698853	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12698856	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12698857	0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12698859	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs12698861	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12698862	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12698864	0.95[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12698865	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12698867	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12698869	0.89[AFR][1000 genomes]
rs12698873	0.92[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs12698875	0.84[AFR][1000 genomes]
rs12698879	0.83[AFR][1000 genomes]
rs12698880	0.81[AFR][1000 genomes]
rs12698882	0.87[ASN][1000 genomes]
rs12698883	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs13229395	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13229686	0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs13231497	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13238017	0.87[ASN][1000 genomes]
rs13242485	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13340492	0.86[ASN][1000 genomes]
rs1404275	0.88[AFR][1000 genomes]
rs1476104	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17365011	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17365333	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17365375	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17462837	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17762460	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs1880369	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs2030705	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs2030706	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs2866275	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs34519726	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35317642	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4318956	0.95[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4475377	0.88[AFR][1000 genomes]
rs4623296	0.96[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs58849135	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6460536	0.81[EUR][1000 genomes]
rs6460539	0.96[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs67847242	0.95[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs6943610	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6943630	0.82[AFR][1000 genomes]
rs6945241	0.85[ASN][1000 genomes]
rs6946066	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6948676	0.90[AFR][1000 genomes]
rs6951909	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6953075	0.86[ASN][1000 genomes]
rs6953170	0.81[EUR][1000 genomes]
rs6962999	0.81[EUR][1000 genomes]
rs6964139	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs6970670	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6971237	0.87[ASN][1000 genomes]
rs6975814	0.86[ASN][1000 genomes]
rs735060	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7779308	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7780640	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7782771	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs7783039	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7783592	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7783748	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7790084	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7791101	0.81[EUR][1000 genomes]
rs7791954	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7796592	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7799192	0.90[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7800317	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7800759	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7803814	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs7806363	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7807263	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs870919	0.89[AFR][1000 genomes]
rs877188	0.91[AFR][1000 genomes]
rs917717	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9638268	0.81[EUR][1000 genomes]
rs9638582	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9647931	0.85[ASN][1000 genomes]
rs9647932	0.84[ASN][1000 genomes]
rs9691023	0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021538	chr7:69130236-69575753	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv538917	chr7:69130236-69575753	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv817276	chr7:69130237-69736834	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1018749	chr7:69149029-69995112	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1018289	chr7:69383450-69650885	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv538922	chr7:69383450-69650885	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv532782	chr7:69383651-70189959	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	esv2758119	chr7:69412504-69594161	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	esv2759536	chr7:69412504-69594161	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv1020488	chr7:69465268-69671126	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv1022932	chr7:69496659-69564369	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv538925	chr7:69496659-69564369	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv1034817	chr7:69507871-69578892	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
14	nsv538926	chr7:69507871-69578892	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
15	nsv1028975	chr7:69513266-69578892	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
16	nsv916345	chr7:69520612-69784809	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1476105	AUTS2	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:69557800-69562800	Weak transcription	Ovary	ovary
2	chr7:69558400-69562600	Weak transcription	Psoas Muscle	Psoas
3	chr7:69558400-69564200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr7:69558800-69562600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr7:69558800-69562800	Weak transcription	Adipose Nuclei	Adipose
6	chr7:69558800-69564000	Weak transcription	Osteobl	bone
7	chr7:69559000-69562800	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr7:69559000-69562800	Weak transcription	HSMM	muscle
9	chr7:69559000-69563200	Weak transcription	Fetal Intestine Large	intestine
10	chr7:69559000-69563400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr7:69559000-69563400	Weak transcription	Brain Cingulate Gyrus	brain
12	chr7:69559000-69563400	Weak transcription	NH-A	brain
13	chr7:69559200-69562600	Weak transcription	Duodenum Mucosa	Duodenum
14	chr7:69559200-69562800	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr7:69559400-69562800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr7:69559600-69563200	Weak transcription	Brain Hippocampus Middle	brain
17	chr7:69559800-69563200	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr7:69560000-69562800	Weak transcription	Fetal Intestine Small	intestine
19	chr7:69560000-69564000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr7:69560200-69562800	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr7:69560200-69562800	Weak transcription	Fetal Muscle Leg	muscle
22	chr7:69560400-69562600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr7:69560400-69562600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr7:69560400-69562600	Weak transcription	Colon Smooth Muscle	Colon
25	chr7:69560400-69562800	Weak transcription	Fetal Stomach	stomach
26	chr7:69560400-69564200	Weak transcription	Rectal Smooth Muscle	rectum
27	chr7:69560400-69564600	Weak transcription	Brain Anterior Caudate	brain
28	chr7:69562000-69562800	Weak transcription	Brain Germinal Matrix	brain
29	chr7:69562000-69562800	Enhancers	Fetal Brain Female	brain
30	chr7:69562000-69565000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr7:69562200-69563000	Enhancers	Pancreatic Islets	Pancreatic Islet
32	chr7:69562200-69564800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr7:69562400-69562600	Flanking Active TSS	Fetal Heart	heart
34	chr7:69562400-69563000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr7:69562400-69563000	Enhancers	Fetal Kidney	kidney
36	chr7:69562400-69564800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr7:69562400-69565400	Enhancers	Fetal Lung	lung

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