Variant report

Variant	rs17040790
Chromosome Location	chr2:50756210-50756211
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr2:50756191-50756267	GM20000	blood:	n/a	n/a

Variant related genes	Relation type
NRXN1	TF binding region

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10169577	1.00[AMR][1000 genomes]
rs10170613	1.00[AMR][1000 genomes]
rs10177472	1.00[AMR][1000 genomes]
rs10190049	1.00[AMR][1000 genomes]
rs10194089	1.00[AMR][1000 genomes]
rs10200688	1.00[AMR][1000 genomes]
rs10205639	1.00[AMR][1000 genomes]
rs10211401	1.00[AMR][1000 genomes]
rs10221724	1.00[AMR][1000 genomes]
rs10221944	1.00[AMR][1000 genomes]
rs11125307	1.00[AMR][1000 genomes]
rs11125308	1.00[AMR][1000 genomes]
rs11125309	1.00[AMR][1000 genomes]
rs11125310	1.00[AMR][1000 genomes]
rs11125312	1.00[AMR][1000 genomes]
rs11125313	1.00[AMR][1000 genomes]
rs13398501	1.00[AMR][1000 genomes]
rs13402154	1.00[AMR][1000 genomes]
rs13402266	1.00[AMR][1000 genomes]
rs13402450	1.00[AMR][1000 genomes]
rs13409159	1.00[AMR][1000 genomes]
rs13409894	1.00[AMR][1000 genomes]
rs13410477	1.00[AMR][1000 genomes]
rs13411836	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs13411953	1.00[AMR][1000 genomes]
rs13420978	1.00[AMR][1000 genomes]
rs13423536	1.00[AMR][1000 genomes]
rs13423656	1.00[AMR][1000 genomes]
rs13423870	1.00[AMR][1000 genomes]
rs13424060	1.00[AMR][1000 genomes]
rs13424091	1.00[AMR][1000 genomes]
rs28631421	1.00[AMR][1000 genomes]
rs6720227	1.00[AMR][1000 genomes]
rs6722766	1.00[AMR][1000 genomes]
rs6722905	1.00[AMR][1000 genomes]
rs6723039	1.00[AMR][1000 genomes]
rs6735456	1.00[AMR][1000 genomes]
rs6735458	1.00[AMR][1000 genomes]
rs6745627	1.00[AMR][1000 genomes]
rs7598865	1.00[AMR][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	nsv492164	chr2:50399251-51029090	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1000653	chr2:50417660-51083470	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv535693	chr2:50417660-51083470	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv948361	chr2:50611076-50785178	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv933786	chr2:50628354-50780185	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv1010510	chr2:50649641-51011565	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv535694	chr2:50649641-51011565	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv532650	chr2:50675808-51136752	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv491644	chr2:50680795-50892906	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv498102	chr2:50680795-50937503	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv532651	chr2:50712339-50758351	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv532681	chr2:50715261-51172182	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv933959	chr2:50722885-50858529	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv915896	chr2:50725664-51057797	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
15	nsv498101	chr2:50725729-50937503	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
16	nsv933706	chr2:50755312-50765504	Active TSS Enhancers Flanking Active TSS Weak transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:50753200-50756600	Weak transcription	Brain Germinal Matrix	brain
2	chr2:50754000-50763200	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr2:50754000-50763400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr2:50756000-50759800	Weak transcription	Fetal Brain Female	brain
5	chr2:50756200-50756800	Enhancers	Cortex derived primary cultured neurospheres	brain

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