Variant report

Variant	rs516214
Chromosome Location	chr13:39973884-39973885
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1010912	1.00[YRI][hapmap]
rs1010913	1.00[YRI][hapmap]
rs1175912	0.81[ASN][1000 genomes]
rs1185800	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs12429365	0.85[JPT][hapmap]
rs1535776	0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1752053	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17803662	0.85[LWK][hapmap];1.00[YRI][hapmap]
rs2182779	1.00[YRI][hapmap]
rs4941926	0.88[GIH][hapmap]
rs561008	0.90[CHB][hapmap];0.93[JPT][hapmap]
rs629011	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs629373	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs641027	0.92[CHB][hapmap];0.93[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	nsv900008	chr13:39962791-40020267	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs516214	LHFP	cis	parietal	SCAN
rs516214	KBTBD6	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:39960000-39979200	Weak transcription	NHDF-Ad	bronchial
2	chr13:39969400-39975400	Weak transcription	Brain Substantia Nigra	brain
3	chr13:39970000-39975200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr13:39970000-39975600	Weak transcription	Fetal Brain Female	brain
5	chr13:39970000-39977200	Weak transcription	Brain Hippocampus Middle	brain
6	chr13:39970200-39975400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr13:39970200-39975600	Weak transcription	Fetal Brain Male	brain
8	chr13:39970200-39979600	Weak transcription	Brain Cingulate Gyrus	brain
9	chr13:39970400-39974800	Weak transcription	Fetal Muscle Trunk	muscle
10	chr13:39970400-39975400	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr13:39970400-39975600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr13:39970400-39976600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr13:39971200-39980200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr13:39971600-39975400	Weak transcription	Rectal Smooth Muscle	rectum
15	chr13:39972000-39974000	Enhancers	Fetal Heart	heart
16	chr13:39972400-39979600	Weak transcription	NHLF	lung
17	chr13:39972800-39975400	Weak transcription	Ovary	ovary
18	chr13:39972800-39988600	Weak transcription	Fetal Muscle Leg	muscle
19	chr13:39973200-39975400	Weak transcription	Right Atrium	heart
20	chr13:39973200-39975400	Weak transcription	Right Ventricle	heart
21	chr13:39973200-39976400	Weak transcription	Left Ventricle	heart
22	chr13:39973200-39977600	Weak transcription	Adipose Nuclei	Adipose

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