Variant report

Variant	rs6448011
Chromosome Location	chr4:21089763-21089764
allele	A/C
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]
rs10007120	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10028465	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10028561	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10029228	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1023722	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs10516376	0.85[JPT][hapmap]
rs10516377	0.85[JPT][hapmap]
rs10938829	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs11944192	0.92[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs11944859	0.85[JPT][hapmap]
rs11944996	0.85[JPT][hapmap]
rs12642991	0.84[ASN][1000 genomes]
rs12643360	0.84[CEU][hapmap];0.92[CHB][hapmap];0.85[JPT][hapmap]
rs12643371	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12646516	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12649352	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12649359	0.84[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs1368640	0.82[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs1425336	0.82[JPT][hapmap]
rs1433493	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1560786	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1560788	0.92[CHB][hapmap];0.85[JPT][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1560789	0.81[CEU][hapmap];0.92[CHB][hapmap];0.85[JPT][hapmap]
rs1560790	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16867638	0.85[JPT][hapmap]
rs16870359	0.88[CEU][hapmap];0.92[CHB][hapmap];0.85[JPT][hapmap]
rs16870421	0.88[CEU][hapmap];0.92[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs16870439	0.84[CHB][hapmap];0.85[JPT][hapmap]
rs16870444	0.84[CHB][hapmap];0.85[JPT][hapmap]
rs16870511	0.82[JPT][hapmap]
rs16870621	0.85[JPT][hapmap]
rs1865193	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1897664	0.84[CEU][hapmap];0.92[CHB][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28390301	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28396704	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28492736	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28718441	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59916150	0.81[EUR][1000 genomes]
rs61277470	0.84[ASN][1000 genomes]
rs6448013	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6448016	0.84[CEU][hapmap];0.92[CHB][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6448018	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6448019	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6814358	0.84[CEU][hapmap];0.92[CHB][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6824763	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6832734	0.85[JPT][hapmap]
rs6858323	0.85[JPT][hapmap]
rs7356370	0.84[CEU][hapmap];0.92[CHB][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7356371	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7667541	0.83[CEU][hapmap];0.92[CHB][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7673495	0.88[CEU][hapmap];0.92[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs7688396	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7689134	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7689193	0.84[CEU][hapmap];0.92[CHB][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7689340	0.83[CEU][hapmap];0.92[CHB][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7694857	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7695039	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7695878	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap]
rs7696284	0.92[CHB][hapmap];0.85[JPT][hapmap]
rs7696531	0.83[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]
rs7696822	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs7696887	0.84[CEU][hapmap];0.92[CHB][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs876477	0.84[CHB][hapmap];0.85[JPT][hapmap]
rs919856	0.92[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];0.85[JPT][hapmap]

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	nsv1014941	chr4:20611726-21345226	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv537053	chr4:20611726-21345226	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv1013365	chr4:20834054-21609078	Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
4	nsv829878	chr4:20966047-21138626	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv878745	chr4:21054348-21155716	Enhancers Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv878746	chr4:21054348-21169062	Enhancers Active TSS Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv878747	chr4:21057794-21169062	Enhancers Active TSS Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv522328	chr4:21083553-21096827	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6448011	LCORL	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:21085800-21089800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr4:21089600-21090600	Enhancers	HUVEC	blood vessel

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