Variant report

Variant	rs7800759
Chromosome Location	chr7:69482645-69482646
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 98 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10499813	0.88[ASN][1000 genomes]
rs12112758	0.82[AFR][1000 genomes]
rs12113555	0.84[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs12667561	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12669794	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12673575	0.83[AFR][1000 genomes]
rs12698815	0.81[AMR][1000 genomes]
rs12698820	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12698826	0.86[AMR][1000 genomes]
rs12698835	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12698838	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12698841	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12698843	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12698846	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12698847	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12698850	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12698851	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12698853	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12698856	0.84[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs12698857	1.00[CHB][hapmap];0.93[JPT][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs12698859	0.89[ASN][1000 genomes]
rs12698861	0.83[AFR][1000 genomes]
rs12698862	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12698864	0.85[AFR][1000 genomes]
rs12698865	0.83[AFR][1000 genomes]
rs12698867	0.83[AFR][1000 genomes]
rs12698869	0.88[ASN][1000 genomes]
rs12698873	0.82[AFR][1000 genomes]
rs12698875	0.86[ASN][1000 genomes]
rs12698879	0.82[ASN][1000 genomes]
rs12698880	0.82[ASN][1000 genomes]
rs13229395	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13231497	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13236841	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs13242485	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13247796	0.92[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs1404275	0.82[ASN][1000 genomes]
rs1476104	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1476105	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17365011	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17365333	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17365375	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17462837	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17604001	0.80[ASN][1000 genomes]
rs1880369	0.88[ASN][1000 genomes]
rs34519726	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35062112	0.82[ASN][1000 genomes]
rs35317642	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4318956	0.84[AFR][1000 genomes]
rs4475377	0.82[ASN][1000 genomes]
rs4623296	0.85[AFR][1000 genomes]
rs58849135	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6460539	0.85[AFR][1000 genomes]
rs67847242	0.85[AFR][1000 genomes]
rs6943610	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6943630	0.86[ASN][1000 genomes]
rs6946066	0.84[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6948676	0.84[ASN][1000 genomes]
rs6951909	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6964139	0.86[ASN][1000 genomes]
rs6970670	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs735060	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7779308	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7780640	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7782771	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7783039	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7783592	0.82[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7783748	0.82[AFR][1000 genomes]
rs7790084	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7791954	0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7796592	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7800317	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7801117	0.81[JPT][hapmap]
rs7803814	0.84[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7807263	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7808588	0.82[ASN][1000 genomes]
rs870919	0.84[ASN][1000 genomes]
rs877188	0.81[AFR][1000 genomes]
rs917717	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9332399	0.81[JPT][hapmap]
rs9638582	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[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	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	nsv607429	chr7:69430748-69553093	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
16	nsv1028705	chr7:69453983-69524628	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
17	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7800759	AUTS2	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:69477200-69490400	Weak transcription	Left Ventricle	heart
2	chr7:69477200-69507600	Weak transcription	Right Atrium	heart
3	chr7:69478600-69491000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:69479200-69483400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr7:69479200-69483400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr7:69479400-69483200	Enhancers	Fetal Lung	lung
7	chr7:69479600-69482800	Enhancers	Fetal Stomach	stomach
8	chr7:69479600-69483200	Enhancers	GM12878-XiMat	blood
9	chr7:69479800-69494000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr7:69480200-69486400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr7:69480800-69482800	Enhancers	Ovary	ovary
12	chr7:69481000-69482800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr7:69481200-69486400	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr7:69481200-69486400	Weak transcription	Fetal Brain Male	brain
15	chr7:69481400-69486400	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr7:69481400-69486400	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr7:69481600-69482800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr7:69481600-69486400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr7:69481600-69486600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr7:69481600-69488400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr7:69482000-69486600	Weak transcription	Fetal Intestine Small	intestine
22	chr7:69482200-69482800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr7:69482200-69482800	Enhancers	Brain Germinal Matrix	brain
24	chr7:69482400-69482800	Enhancers	H1 Cell Line	embryonic stem cell
25	chr7:69482400-69482800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr7:69482400-69482800	Enhancers	Duodenum Smooth Muscle	Duodenum
27	chr7:69482400-69482800	Enhancers	Fetal Brain Female	brain
28	chr7:69482400-69482800	Enhancers	Fetal Muscle Leg	muscle
29	chr7:69482400-69486400	Weak transcription	Fetal Heart	heart
30	chr7:69482600-69486400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr7:69482600-69486400	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr7:69482600-69488000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr7:69482600-69490400	Weak transcription	Fetal Thymus	thymus
34	chr7:69482600-69491000	Weak transcription	Psoas Muscle	Psoas

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