Variant report

Variant	rs9454286
Chromosome Location	chr6:68505950-68505951
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:68500812..68503514-chr6:68505426..68509054,4	K562	blood:
2	chr6:68500812..68503276-chr6:68505426..68509268,3	K562	blood:

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10223522	0.91[ASN][1000 genomes]
rs10223623	0.91[ASN][1000 genomes]
rs11750959	0.81[EUR][1000 genomes]
rs12214983	0.91[YRI][hapmap];0.86[AFR][1000 genomes]
rs12524662	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13200085	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13215798	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1606681	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1606684	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16880598	0.89[ASN][1000 genomes]
rs1913477	0.81[EUR][1000 genomes]
rs1913478	0.81[EUR][1000 genomes]
rs2063737	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34124069	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34125381	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34528887	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34909337	0.89[ASN][1000 genomes]
rs35459134	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4259236	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56285162	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57219296	0.91[ASN][1000 genomes]
rs6455248	1.00[ASN][1000 genomes]
rs6455250	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6901396	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6901505	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6906512	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6910355	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6913405	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6913540	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6914109	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6920063	0.91[ASN][1000 genomes]
rs6925379	0.91[ASN][1000 genomes]
rs6925414	0.91[ASN][1000 genomes]
rs6927559	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6933002	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6933191	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6933666	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6940575	0.91[ASN][1000 genomes]
rs6941472	0.91[ASN][1000 genomes]
rs73444607	0.91[ASN][1000 genomes]
rs73444610	0.91[ASN][1000 genomes]
rs73444633	0.89[ASN][1000 genomes]
rs73446734	1.00[ASN][1000 genomes]
rs73462635	0.94[ASN][1000 genomes]
rs73462660	1.00[ASN][1000 genomes]
rs7741697	1.00[ASN][1000 genomes]
rs7750694	0.91[ASN][1000 genomes]
rs7755118	0.91[ASN][1000 genomes]
rs7756292	0.91[ASN][1000 genomes]
rs7760466	0.91[ASN][1000 genomes]
rs7763531	1.00[ASN][1000 genomes]
rs7765314	0.91[ASN][1000 genomes]
rs7769657	0.91[ASN][1000 genomes]
rs9294775	1.00[ASN][1000 genomes]
rs9294776	1.00[ASN][1000 genomes]
rs9445916	1.00[ASN][1000 genomes]
rs9445917	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9454284	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9454287	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9454301	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1027923	chr6:67830533-68828337	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv1016471	chr6:67854363-68708368	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv538292	chr6:67854363-68708368	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv603589	chr6:67975166-68865718	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	esv2759439	chr6:68156441-68526511	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	esv2757176	chr6:68269956-68526511	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv886115	chr6:68341629-68644319	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv886116	chr6:68356291-68607744	Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv886117	chr6:68380125-68526511	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv886120	chr6:68384242-68509062	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv886121	chr6:68384242-68526511	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv886122	chr6:68397567-68526511	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv603593	chr6:68410039-68509062	ZNF genes & repeats Weak transcription Active TSS Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	nsv603594	chr6:68417147-68509062	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	esv34754	chr6:68417692-68532979	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	nsv886125	chr6:68423329-68526511	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
17	nsv886126	chr6:68449430-68526511	Weak transcription Enhancers ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
18	nsv1032151	chr6:68455238-68509030	Enhancers Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
19	nsv463144	chr6:68470086-68563328	Weak transcription Enhancers ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
20	nsv603596	chr6:68470086-68563328	Enhancers ZNF genes & repeats Active TSS Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
21	nsv1026831	chr6:68486914-68509030	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
22	nsv603597	chr6:68499138-68542695	Enhancers ZNF genes & repeats Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
23	nsv463145	chr6:68505842-68549473	Active TSS Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	n/a
24	nsv603598	chr6:68505842-68549473	Weak transcription Enhancers Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9454286	LINGO3	trans	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:68505000-68506200	Enhancers	ES-I3 Cell Line	embryonic stem cell
2	chr6:68505200-68506000	Enhancers	H9 Cell Line	embryonic stem cell
3	chr6:68505200-68506000	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr6:68505200-68506000	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr6:68505200-68506000	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr6:68505400-68506400	Enhancers	K562	blood
7	chr6:68505600-68506000	Enhancers	iPS-20b Cell Line	embryonic stem cell

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