Variant report

Variant	rs1820544
Chromosome Location	chr12:40793993-40793994
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	12:40793507-40812339..12:40836437-40839614	H1-hESC	embryonic stem cell:	embryo

Variant related genes	Relation type
ENSG00000258167	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1019709	0.84[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs10459265	0.85[JPT][hapmap]
rs10467146	0.81[JPT][hapmap]
rs10735934	0.85[JPT][hapmap]
rs10784548	0.81[JPT][hapmap]
rs10784585	0.82[JPT][hapmap]
rs10784589	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10784595	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10784596	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10878441	0.80[JPT][hapmap]
rs10878507	0.94[AFR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10878551	0.86[CHB][hapmap]
rs10878552	0.86[CHB][hapmap]
rs11176421	0.81[ASN][1000 genomes]
rs11176495	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12426362	0.81[JPT][hapmap]
rs17466605	0.81[JPT][hapmap]
rs1820545	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2081700	0.92[ASN][1000 genomes]
rs2081701	0.91[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs2404840	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2896982	0.90[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs3761863	0.81[JPT][hapmap]
rs4280068	0.92[ASN][1000 genomes]
rs4351885	0.92[ASN][1000 genomes]
rs4768236	0.81[JPT][hapmap]
rs4768237	0.81[JPT][hapmap]
rs6581667	0.85[JPT][hapmap]
rs6581668	0.85[JPT][hapmap]
rs7137809	0.92[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];0.99[ASN][1000 genomes]
rs7307562	0.86[JPT][hapmap]
rs7308560	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7310390	0.95[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs7954318	0.92[ASN][1000 genomes]
rs7956721	0.86[CHB][hapmap];0.80[GIH][hapmap]
rs7968721	0.93[ASN][1000 genomes]
rs7972535	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.90[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7975124	0.90[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs994798	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832377	chr12:40704881-40855223	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv899032	chr12:40735939-40827479	Weak transcription ZNF genes & repeats Strong transcription Enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv558598	chr12:40742363-40828264	Strong transcription Weak transcription Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	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
5	nsv1047639	chr12:40774370-40804386	Enhancers Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv558599	chr12:40790698-40814452	Enhancers Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1820544	CNTN1	cis	cerebellum	SCAN
rs1820544	TIPIN	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40787200-40799200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:40793800-40799400	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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