Variant report

Variant	rs1873674
Chromosome Location	chr12:40930284-40930285
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CNTN1-1	chr12:40930242-40930286	XLOC_009713
2	lnc-CNTN1-1	chr12:40930242-40930286	NONHSAT027736

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1122621	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1122863	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11564109	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11829565	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11835808	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1427262	1.00[JPT][hapmap]
rs1492328	1.00[ASN][1000 genomes]
rs1492329	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1492337	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1492338	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17128391	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17128401	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17128416	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17444709	1.00[JPT][hapmap]
rs17529964	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs17532278	0.81[EUR][1000 genomes]
rs17533153	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17533321	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17589334	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs17598093	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17598156	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17599001	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17599042	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17599666	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17600388	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1844979	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1844982	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4767980	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4767983	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4768261	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768265	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768276	0.80[AMR][1000 genomes]
rs4768287	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768288	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768289	0.82[EUR][1000 genomes]
rs4768291	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs55642775	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55649806	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55818225	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56036709	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56211973	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56226314	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56952712	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57161116	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59005564	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59095251	1.00[ASN][1000 genomes]
rs59367732	1.00[ASN][1000 genomes]
rs7309042	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs73094611	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73100423	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73100426	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73100438	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73106618	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73106620	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73106623	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73110070	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73110091	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73112007	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73112026	1.00[ASN][1000 genomes]
rs73114284	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73116206	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73119908	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7315186	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7959536	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7960976	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899033	chr12:40758652-41122288	Bivalent/Poised TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv8970	chr12:40904094-40951213	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	esv3388339	chr12:40917344-40931738	Enhancers Weak transcription	TF binding region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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