Variant report

Variant	rs12698826
Chromosome Location	chr7:69425893-69425894
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 79 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1008379	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12112758	0.90[ASN][1000 genomes]
rs12667561	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12669794	0.92[ASN][1000 genomes]
rs12673575	0.90[ASN][1000 genomes]
rs12698812	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12698814	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12698815	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12698820	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12698835	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12698838	0.85[AMR][1000 genomes]
rs12698841	0.85[AMR][1000 genomes]
rs12698843	0.82[AMR][1000 genomes]
rs12698847	0.83[AMR][1000 genomes]
rs12698851	0.88[ASN][1000 genomes]
rs12698861	0.88[ASN][1000 genomes]
rs12698864	0.86[ASN][1000 genomes]
rs12698865	0.90[ASN][1000 genomes]
rs12698867	0.90[ASN][1000 genomes]
rs12698873	0.88[ASN][1000 genomes]
rs13228464	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13229395	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs13231497	0.83[AMR][1000 genomes]
rs13236841	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13242485	0.83[AMR][1000 genomes]
rs1476105	0.92[ASN][1000 genomes]
rs17353815	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17365333	0.83[AMR][1000 genomes]
rs17365375	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs17458097	0.89[AMR][1000 genomes]
rs17462837	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2159679	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2903097	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34519726	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs35317642	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs35322474	0.88[AMR][1000 genomes]
rs4318956	0.88[ASN][1000 genomes]
rs4623296	0.88[ASN][1000 genomes]
rs60739014	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6460539	0.87[ASN][1000 genomes]
rs67847242	0.90[ASN][1000 genomes]
rs6951909	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6963101	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6970670	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs735060	0.83[AMR][1000 genomes]
rs763759	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7779308	0.85[AMR][1000 genomes]
rs7780640	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7781403	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7783039	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7783748	0.88[ASN][1000 genomes]
rs7790084	0.80[AMR][1000 genomes]
rs7799192	0.90[ASN][1000 genomes]
rs7800317	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7800759	0.86[AMR][1000 genomes]
rs7801117	0.82[CEU][hapmap]
rs7808773	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs917717	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9332399	0.82[CEU][hapmap]
rs9638575	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9638582	0.83[AMR][1000 genomes]
rs9691023	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 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	nsv492242	chr7:69330737-69520566	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv916265	chr7:69367265-69433076	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv1031593	chr7:69367316-69445052	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	nsv538921	chr7:69367316-69445052	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
9	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
10	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
11	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
12	nsv1034281	chr7:69403828-69548378	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv538923	chr7:69403828-69548378	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv1034182	chr7:69406172-69529294	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv538924	chr7:69406172-69529294	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
16	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
17	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12698826	AUTS2	cis	cerebellum	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:69404600-69427800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr7:69411000-69426800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr7:69415000-69427200	Weak transcription	Fetal Kidney	kidney
4	chr7:69418000-69427000	Weak transcription	Adipose Nuclei	Adipose
5	chr7:69418600-69426800	Weak transcription	Brain Angular Gyrus	brain
6	chr7:69418600-69427000	Weak transcription	Brain Cingulate Gyrus	brain
7	chr7:69418800-69426800	Weak transcription	Brain Anterior Caudate	brain
8	chr7:69419600-69426800	Weak transcription	Fetal Stomach	stomach
9	chr7:69420400-69426800	Weak transcription	GM12878-XiMat	blood
10	chr7:69421000-69426400	Weak transcription	Dnd41	blood
11	chr7:69421400-69426800	Weak transcription	Primary T cells from cord blood	blood
12	chr7:69422600-69427600	Enhancers	Fetal Heart	heart
13	chr7:69423800-69426000	Weak transcription	Right Atrium	heart
14	chr7:69423800-69426800	Weak transcription	Right Ventricle	heart
15	chr7:69423800-69426800	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr7:69423800-69427000	Weak transcription	Fetal Muscle Leg	muscle
17	chr7:69423800-69427000	Weak transcription	Left Ventricle	heart
18	chr7:69423800-69428400	Enhancers	Brain Germinal Matrix	brain
19	chr7:69424000-69426800	Weak transcription	Fetal Thymus	thymus
20	chr7:69424000-69427200	Weak transcription	Primary B cells from cord blood	blood
21	chr7:69424200-69426800	Weak transcription	Primary hematopoietic stem cells	blood
22	chr7:69424200-69427000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr7:69424400-69427000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr7:69424400-69427000	Enhancers	Fetal Brain Male	brain
25	chr7:69424600-69426200	Weak transcription	Colon Smooth Muscle	Colon
26	chr7:69424600-69426800	Weak transcription	Primary B cells from peripheral blood	blood
27	chr7:69424600-69426800	Weak transcription	Psoas Muscle	Psoas
28	chr7:69424800-69427200	Enhancers	Fetal Brain Female	brain
29	chr7:69425000-69426000	Weak transcription	Stomach Smooth Muscle	stomach
30	chr7:69425000-69426800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr7:69425000-69427000	Weak transcription	Brain Substantia Nigra	brain
32	chr7:69425200-69426600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr7:69425200-69426800	Weak transcription	Brain Hippocampus Middle	brain
34	chr7:69425200-69427400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr7:69425400-69426000	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr7:69425400-69426600	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr7:69425400-69428800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr7:69425600-69427000	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr7:69425800-69427000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr7:69425800-69427200	Enhancers	Thymus	Thymus
41	chr7:69425800-69430000	Enhancers	Fetal Intestine Small	intestine

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