Variant report

Variant	rs13228464
Chromosome Location	chr7:69346385-69346386
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1008379	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10085775	0.82[ASN][1000 genomes]
rs10237145	0.82[ASN][1000 genomes]
rs10241485	0.82[ASN][1000 genomes]
rs11765886	0.80[ASN][1000 genomes]
rs12698812	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12698814	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12698815	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12698820	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12698826	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12698838	0.81[ASN][1000 genomes]
rs12698841	0.81[ASN][1000 genomes]
rs12698843	0.80[ASN][1000 genomes]
rs12698846	0.80[ASN][1000 genomes]
rs12698847	0.80[ASN][1000 genomes]
rs12698850	0.80[ASN][1000 genomes]
rs12698853	0.80[ASN][1000 genomes]
rs13231497	0.81[ASN][1000 genomes]
rs13232095	0.89[ASN][1000 genomes]
rs13236841	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13242485	0.81[ASN][1000 genomes]
rs1476104	0.80[ASN][1000 genomes]
rs17353815	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17365011	0.84[ASN][1000 genomes]
rs17365333	0.80[ASN][1000 genomes]
rs17458097	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2058395	0.82[ASN][1000 genomes]
rs210598	0.86[ASN][1000 genomes]
rs210600	0.82[ASN][1000 genomes]
rs210603	0.82[ASN][1000 genomes]
rs2159679	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2903097	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34249708	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35322474	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4717521	0.82[ASN][1000 genomes]
rs521259	0.82[ASN][1000 genomes]
rs585282	0.81[JPT][hapmap]
rs595681	0.81[JPT][hapmap]
rs60739014	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs608796	0.86[ASN][1000 genomes]
rs610930	0.81[JPT][hapmap]
rs622767	0.86[ASN][1000 genomes]
rs6460532	0.81[EUR][1000 genomes]
rs6943610	0.80[ASN][1000 genomes]
rs6955261	0.81[EUR][1000 genomes]
rs6955815	0.82[ASN][1000 genomes]
rs6959766	0.86[ASN][1000 genomes]
rs6963101	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6974004	0.82[ASN][1000 genomes]
rs735060	0.80[ASN][1000 genomes]
rs763759	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7779010	0.81[EUR][1000 genomes]
rs7779308	0.81[ASN][1000 genomes]
rs7781403	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7783039	0.81[AMR][1000 genomes]
rs7790084	0.80[ASN][1000 genomes]
rs7793984	0.82[ASN][1000 genomes]
rs7796592	0.83[ASN][1000 genomes]
rs7800317	0.81[AMR][1000 genomes]
rs7801117	0.82[CEU][hapmap];0.81[JPT][hapmap]
rs7808773	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9332399	0.82[CEU][hapmap];0.81[JPT][hapmap]
rs9638575	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9638582	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831021	chr7:69122169-69364491	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	nsv1017390	chr7:69339404-69406232	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv538920	chr7:69339404-69406232	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13228464	AUTS2	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:69311400-69371600	Weak transcription	Primary B cells from cord blood	blood
2	chr7:69337600-69354600	Weak transcription	Stomach Smooth Muscle	stomach
3	chr7:69338400-69350600	Weak transcription	Brain Anterior Caudate	brain
4	chr7:69338400-69367200	Weak transcription	Primary hematopoietic stem cells	blood
5	chr7:69343600-69350400	Weak transcription	Brain Substantia Nigra	brain
6	chr7:69343600-69354200	Weak transcription	Brain Angular Gyrus	brain
7	chr7:69344000-69354800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr7:69344600-69346400	Enhancers	Fetal Thymus	thymus
9	chr7:69344800-69347600	Enhancers	Primary B cells from peripheral blood	blood
10	chr7:69345000-69346400	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr7:69345000-69346800	Enhancers	Thymus	Thymus
12	chr7:69345200-69346600	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr7:69345400-69346600	Weak transcription	Fetal Brain Male	brain
14	chr7:69345400-69347400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr7:69345400-69350600	Weak transcription	Fetal Stomach	stomach
16	chr7:69345600-69346400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr7:69345600-69346600	Enhancers	Fetal Brain Female	brain
18	chr7:69345600-69348000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr7:69345800-69347800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr7:69346000-69346400	Weak transcription	Brain Germinal Matrix	brain
21	chr7:69346000-69347800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr7:69346000-69349400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr7:69346200-69348200	Enhancers	GM12878-XiMat	blood
24	chr7:69346200-69350200	Weak transcription	Colon Smooth Muscle	Colon

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