Variant report

Variant	rs9576777
Chromosome Location	chr13:39896154-39896155
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs12856032	0.82[EUR][1000 genomes]
rs1333439	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1924315	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2025410	0.86[EUR][1000 genomes]
rs2147127	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2147130	0.81[JPT][hapmap]
rs2324258	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2985186	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4340188	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6563698	0.82[CHB][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.84[TSI][hapmap]
rs7318557	1.00[CEU][hapmap];0.88[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7321424	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7335060	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7338314	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs746076	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs747383	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7986707	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7988864	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7990125	0.81[JPT][hapmap]
rs7995844	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9285131	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9315671	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9315675	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9532371	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9532372	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9548722	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9548729	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9548731	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9548733	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9548738	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs957184	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9576776	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs987848	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[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
rs9576777	LHFP	cis	parietal	SCAN
rs9576777	MRPS31	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:39886400-39896600	Weak transcription	Aorta	Aorta
2	chr13:39891000-39899200	Weak transcription	Fetal Heart	heart
3	chr13:39891800-39896200	Weak transcription	Brain Anterior Caudate	brain
4	chr13:39892000-39896400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr13:39892000-39896400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr13:39892000-39896600	Weak transcription	Brain Cingulate Gyrus	brain
7	chr13:39892000-39897200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr13:39892200-39896200	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr13:39892200-39901200	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr13:39893000-39898400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr13:39893400-39897600	Enhancers	Adipose Nuclei	Adipose
12	chr13:39893600-39899000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr13:39893800-39899000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr13:39894200-39899000	Weak transcription	Right Ventricle	heart
15	chr13:39894200-39899000	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr13:39894400-39899000	Weak transcription	Left Ventricle	heart
17	chr13:39894600-39898800	Weak transcription	Lung	lung
18	chr13:39894600-39899000	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr13:39894800-39897200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr13:39895200-39896600	Enhancers	Ovary	ovary
21	chr13:39895200-39897200	Weak transcription	Fetal Stomach	stomach
22	chr13:39895400-39899000	Weak transcription	Right Atrium	heart
23	chr13:39895600-39898000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr13:39895800-39896600	Enhancers	Brain Angular Gyrus	brain
25	chr13:39895800-39896600	Enhancers	Duodenum Smooth Muscle	Duodenum
26	chr13:39895800-39897000	Enhancers	Brain Hippocampus Middle	brain
27	chr13:39895800-39897600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr13:39895800-39897800	Enhancers	Brain Substantia Nigra	brain
29	chr13:39896000-39896200	Enhancers	Fetal Lung	lung
30	chr13:39896000-39899200	Weak transcription	Fetal Muscle Leg	muscle

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