Variant report

Variant	rs12517268
Chromosome Location	chr5:15925234-15925235
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10520827	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12522838	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];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3935971	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[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72736151	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv880755	chr5:15670377-15938553	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1031483	chr5:15738485-15926083	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	nsv461986	chr5:15854098-15943683	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
4	nsv597292	chr5:15854098-15943683	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
5	nsv830216	chr5:15860662-16060420	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
6	nsv427712	chr5:15883439-16055856	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
7	nsv4735	chr5:15916346-15961432	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12517268	L1TD1	trans	lymphoblastoid	seeQTL

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:15913800-15936000	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr5:15914000-15926800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr5:15914000-15940000	Weak transcription	Colon Smooth Muscle	Colon
4	chr5:15914600-15928200	Weak transcription	Fetal Brain Male	brain
5	chr5:15915000-15928000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr5:15919000-15926800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr5:15919000-15926800	Weak transcription	Brain Anterior Caudate	brain
8	chr5:15919000-15926800	Weak transcription	Brain Hippocampus Middle	brain
9	chr5:15919000-15926800	Weak transcription	Brain Substantia Nigra	brain
10	chr5:15919000-15928000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr5:15919000-15928200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr5:15919200-15928200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr5:15919400-15927600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr5:15919600-15933600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr5:15920000-15926600	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr5:15920000-15933400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr5:15920200-15926800	Weak transcription	Fetal Lung	lung
18	chr5:15920400-15928000	Weak transcription	Fetal Stomach	stomach
19	chr5:15922800-15928000	Weak transcription	Ovary	ovary
20	chr5:15923200-15929200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr5:15923400-15927200	Weak transcription	Fetal Brain Female	brain
22	chr5:15924200-15928200	Weak transcription	Esophagus	oesophagus
23	chr5:15924400-15926800	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr5:15924800-15925600	Enhancers	Right Ventricle	heart
25	chr5:15925000-15925800	Enhancers	Fetal Heart	heart
26	chr5:15925200-15927400	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr5:15925200-15928200	Weak transcription	Left Ventricle	heart
28	chr5:15925200-15928400	Weak transcription	Adipose Nuclei	Adipose

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