Variant report

Variant	rs9594331
Chromosome Location	chr13:39961128-39961129
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10467465	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1175906	0.81[GIH][hapmap];1.00[JPT][hapmap]
rs17059768	1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17059778	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.89[MKK][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17059793	0.87[CHD][hapmap];0.88[GIH][hapmap]
rs17803662	1.00[CHD][hapmap];0.88[GIH][hapmap]
rs496665	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58009597	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs629373	1.00[CHD][hapmap]
rs73453070	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7989667	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7990626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9594330	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9603527	1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9603529	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9603530	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9603531	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9805148	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9594331	LHFP	cis	lymphoblastoid	seeQTL

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:39958400-39962200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr13:39958600-39962000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr13:39958600-39962000	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr13:39958800-39961200	Enhancers	Brain Hippocampus Middle	brain
5	chr13:39958800-39963800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr13:39959000-39961200	Enhancers	Right Ventricle	heart
7	chr13:39959000-39961400	Enhancers	Ovary	ovary
8	chr13:39959000-39961600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr13:39959400-39961200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr13:39959400-39961200	Enhancers	Fetal Heart	heart
11	chr13:39959400-39962000	Enhancers	Rectal Smooth Muscle	rectum
12	chr13:39959400-39965800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr13:39959600-39962200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr13:39959600-39968800	Weak transcription	Adipose Nuclei	Adipose
15	chr13:39959800-39963000	Weak transcription	Right Atrium	heart
16	chr13:39960000-39961800	Weak transcription	Aorta	Aorta
17	chr13:39960000-39979200	Weak transcription	NHDF-Ad	bronchial
18	chr13:39960400-39961400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
19	chr13:39960400-39961400	Enhancers	Left Ventricle	heart
20	chr13:39960600-39961200	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr13:39960600-39968800	Weak transcription	Brain Anterior Caudate	brain
22	chr13:39960600-39969000	Weak transcription	Brain Germinal Matrix	brain
23	chr13:39960800-39961600	Weak transcription	Fetal Lung	lung
24	chr13:39960800-39962000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr13:39960800-39968000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr13:39960800-39969000	Weak transcription	Osteobl	bone

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