Variant report

Variant	rs17803327
Chromosome Location	chr13:39958104-39958105
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10492739	1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1185800	0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs12428389	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12429365	0.81[ASN][1000 genomes]
rs561008	0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs629422	0.81[ASN][1000 genomes]
rs641027	0.81[GIH][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs73173498	0.81[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	esv2754118	chr13:39347702-40222644	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1054600	chr13:39801283-40545027	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
3	nsv1036674	chr13:39841482-40008117	Bivalent Enhancer Genic enhancers Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17803327	LHFP	cis	parietal	SCAN
rs17803327	KBTBD6	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:39939600-39959600	Weak transcription	Brain Cingulate Gyrus	brain
2	chr13:39939800-39959800	Weak transcription	Fetal Lung	lung
3	chr13:39945400-39959000	Weak transcription	Brain Substantia Nigra	brain
4	chr13:39946000-39959000	Weak transcription	NHDF-Ad	bronchial
5	chr13:39947600-39959000	Weak transcription	Right Atrium	heart
6	chr13:39947600-39960600	Weak transcription	Fetal Muscle Leg	muscle
7	chr13:39947800-39959400	Weak transcription	Fetal Heart	heart
8	chr13:39950600-39958400	Weak transcription	Adipose Nuclei	Adipose
9	chr13:39952800-39959200	Weak transcription	Brain Anterior Caudate	brain
10	chr13:39954200-39959000	Weak transcription	Right Ventricle	heart
11	chr13:39954400-39959200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr13:39954400-39959600	Weak transcription	Osteobl	bone
13	chr13:39954600-39958400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr13:39954600-39959000	Weak transcription	NH-A	brain
15	chr13:39954600-39959400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr13:39955600-39959000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr13:39955800-39959000	Weak transcription	Left Ventricle	heart
18	chr13:39956200-39958600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr13:39957400-39958200	Enhancers	Ovary	ovary
20	chr13:39957600-39959200	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr13:39957800-39958200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
22	chr13:39957800-39958400	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr13:39957800-39959000	Weak transcription	Aorta	Aorta
24	chr13:39958000-39959400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
25	chr13:39958000-39959400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
26	chr13:39958000-39960000	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
27	chr13:39958000-39960800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell

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