Variant report

Variant	rs1175906
Chromosome Location	chr13:39951039-39951040
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10467465	0.81[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs17059768	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs17059778	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs41286955	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs496665	0.83[ASN][1000 genomes]
rs58009597	0.83[ASN][1000 genomes]
rs73453070	0.83[ASN][1000 genomes]
rs7989667	0.83[ASN][1000 genomes]
rs7990626	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs9594330	0.83[ASN][1000 genomes]
rs9594331	0.81[GIH][hapmap];1.00[JPT][hapmap]
rs9603527	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs9603529	0.83[ASN][1000 genomes]
rs9603530	0.81[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs9603531	0.83[ASN][1000 genomes]
rs9805148	0.83[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
rs1175906	LHFP	cis	lymphoblastoid	seeQTL

Chromatin state (count:28 , 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	chr13:39940200-39953800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr13:39940600-39953800	Weak transcription	Osteobl	bone
5	chr13:39943200-39953800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr13:39944400-39957400	Weak transcription	Fetal Muscle Trunk	muscle
7	chr13:39945000-39954400	Weak transcription	HSMMtube	muscle
8	chr13:39945400-39951800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr13:39945400-39953800	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr13:39945400-39959000	Weak transcription	Brain Substantia Nigra	brain
11	chr13:39946000-39959000	Weak transcription	NHDF-Ad	bronchial
12	chr13:39947600-39959000	Weak transcription	Right Atrium	heart
13	chr13:39947600-39960600	Weak transcription	Fetal Muscle Leg	muscle
14	chr13:39947800-39957400	Weak transcription	Ovary	ovary
15	chr13:39947800-39959400	Weak transcription	Fetal Heart	heart
16	chr13:39948600-39953600	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr13:39948600-39954200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr13:39949600-39954400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr13:39949800-39951800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr13:39949800-39952400	Weak transcription	Left Ventricle	heart
21	chr13:39950200-39952600	Weak transcription	Brain Anterior Caudate	brain
22	chr13:39950400-39951200	Enhancers	Right Ventricle	heart
23	chr13:39950400-39954000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr13:39950600-39958400	Weak transcription	Adipose Nuclei	Adipose
25	chr13:39951000-39951200	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr13:39951000-39951200	Flanking Active TSS	Aorta	Aorta
27	chr13:39951000-39951400	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr13:39951000-39952800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links