Variant report

Variant	rs6978919
Chromosome Location	chr7:69735671-69735672
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 95 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10085696	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1014059	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10258962	0.83[AMR][1000 genomes]
rs10262697	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10499813	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12112638	0.81[AMR][1000 genomes]
rs12113555	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12155144	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12673575	0.84[EUR][1000 genomes]
rs12698838	0.84[ASN][1000 genomes]
rs12698841	0.84[ASN][1000 genomes]
rs12698843	0.85[ASN][1000 genomes]
rs12698846	0.85[ASN][1000 genomes]
rs12698847	0.85[ASN][1000 genomes]
rs12698850	0.83[ASN][1000 genomes]
rs12698853	0.87[ASN][1000 genomes]
rs12698856	0.88[ASN][1000 genomes]
rs12698857	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12698859	0.85[ASN][1000 genomes]
rs12698861	0.82[EUR][1000 genomes]
rs12698862	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12698864	0.83[EUR][1000 genomes]
rs12698865	0.85[EUR][1000 genomes]
rs12698867	0.85[EUR][1000 genomes]
rs12698869	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12698875	0.90[ASN][1000 genomes]
rs12698879	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12698880	0.95[ASN][1000 genomes]
rs12698882	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12698883	0.80[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs12698884	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12698886	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12698892	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12698893	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12698895	0.81[JPT][hapmap]
rs13229686	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13231497	0.84[ASN][1000 genomes]
rs13238017	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13242485	0.84[ASN][1000 genomes]
rs13247796	0.84[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs13340492	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1404275	0.95[ASN][1000 genomes]
rs1476104	0.85[ASN][1000 genomes]
rs17365011	0.81[ASN][1000 genomes]
rs17365333	0.85[ASN][1000 genomes]
rs17604001	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17762460	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1880369	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2030705	0.80[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs2030706	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2866275	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35062112	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4318956	0.83[EUR][1000 genomes]
rs4475377	0.95[ASN][1000 genomes]
rs4623296	0.83[EUR][1000 genomes]
rs6460539	0.84[EUR][1000 genomes]
rs66936223	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs67847242	0.85[EUR][1000 genomes]
rs6943610	0.85[ASN][1000 genomes]
rs6943630	0.86[ASN][1000 genomes]
rs6945241	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6946066	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6948676	0.88[ASN][1000 genomes]
rs6953075	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6964139	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6971237	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6975814	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6978841	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs735060	0.85[ASN][1000 genomes]
rs7779308	0.84[ASN][1000 genomes]
rs7782771	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7783039	0.81[ASN][1000 genomes]
rs7783592	0.88[ASN][1000 genomes]
rs7783748	0.81[EUR][1000 genomes]
rs7790084	0.85[ASN][1000 genomes]
rs7791954	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7792964	0.82[AMR][1000 genomes]
rs7796592	0.82[ASN][1000 genomes]
rs7799192	0.84[EUR][1000 genomes]
rs7803814	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7807263	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7808588	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs870919	0.88[ASN][1000 genomes]
rs877188	0.85[EUR][1000 genomes]
rs9638582	0.85[ASN][1000 genomes]
rs9647931	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9647932	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][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	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
2	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
3	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
4	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
5	nsv869342	chr7:69671501-69958576	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv607431	chr7:69699074-69828729	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv888337	chr7:69707076-69952187	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv529669	chr7:69709373-69974708	Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3'	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
rs6978919	AUTS2	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:69729800-69736000	Weak transcription	Ovary	ovary
2	chr7:69731200-69736000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr7:69733000-69736800	Enhancers	iPS-18 Cell Line	embryonic stem cell
4	chr7:69734600-69735800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr7:69734600-69737800	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr7:69734800-69737800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr7:69735200-69735800	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr7:69735200-69736000	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr7:69735200-69736000	Enhancers	H1 Cell Line	embryonic stem cell
10	chr7:69735200-69736200	Enhancers	H9 Cell Line	embryonic stem cell
11	chr7:69735400-69736000	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr7:69735600-69736000	Enhancers	iPS-20b Cell Line	embryonic stem cell

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