Variant report

Variant	rs11836971
Chromosome Location	chr12:7655278-7655279
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10743939	0.92[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.92[MKK][hapmap];0.92[TSI][hapmap];0.96[ASN][1000 genomes]
rs10772428	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10845306	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11054180	0.87[ASN][1000 genomes]
rs11054214	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11054259	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12809680	0.95[ASN][1000 genomes]
rs12810262	0.96[ASN][1000 genomes]
rs3210140	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4883264	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7307454	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7965049	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv557269	chr12:7623724-7691134	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv1041155	chr12:7655137-7821891	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1045650	chr12:7655137-7824995	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11836971	CD69	cis	cerebellum	SCAN
rs11836971	CLEC4E	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:7650600-7657000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
2	chr12:7652600-7656400	Active TSS	Adipose Nuclei	Adipose
3	chr12:7653200-7656200	Active TSS	Duodenum Smooth Muscle	Duodenum
4	chr12:7653800-7655400	Active TSS	Duodenum Mucosa	Duodenum
5	chr12:7653800-7656200	Active TSS	Fetal Muscle Leg	muscle
6	chr12:7654000-7655800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr12:7654200-7655400	Weak transcription	Liver	Liver
8	chr12:7654600-7656200	Active TSS	Placenta	Placenta
9	chr12:7655000-7655600	Active TSS	Left Ventricle	heart
10	chr12:7655000-7656200	Active TSS	Right Atrium	heart
11	chr12:7655000-7656400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
12	chr12:7655200-7656000	Active TSS	Rectal Mucosa Donor 29	rectum

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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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