Variant report

Variant	rs9603532
Chromosome Location	chr13:39983072-39983073
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs17803662	1.00[ASW][hapmap]
rs9315682	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9315683	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9532376	0.85[JPT][hapmap]
rs9566424	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9566430	0.85[JPT][hapmap]
rs9576782	0.86[CEU][hapmap]
rs9576788	0.84[CEU][hapmap]
rs9576797	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	esv16099	chr13:39982147-39983164	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9603532	LHFP	cis	lymphoblastoid	seeQTL
rs9603532	FREM2	cis	parietal	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:39972800-39988600	Weak transcription	Fetal Muscle Leg	muscle
2	chr13:39975800-39988400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr13:39975800-39988600	Weak transcription	Right Atrium	heart
4	chr13:39976200-39984000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr13:39976600-39990600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr13:39977000-39987800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr13:39977200-39983800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr13:39977400-39983600	Weak transcription	Brain Hippocampus Middle	brain
9	chr13:39977800-39984400	Weak transcription	Psoas Muscle	Psoas
10	chr13:39979400-39983600	Weak transcription	Fetal Brain Male	brain
11	chr13:39980000-39983600	Weak transcription	Brain Anterior Caudate	brain
12	chr13:39980000-39983600	Weak transcription	Fetal Lung	lung
13	chr13:39980000-39983800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr13:39980000-39983800	Weak transcription	NHDF-Ad	bronchial
15	chr13:39980000-39984000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr13:39980000-39984000	Weak transcription	NHLF	lung
17	chr13:39980200-39983200	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr13:39980200-39983200	Weak transcription	Brain Angular Gyrus	brain
19	chr13:39980200-39983600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr13:39980200-39983600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr13:39980200-39983800	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr13:39980200-39984400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr13:39980200-39988600	Weak transcription	Fetal Stomach	stomach
24	chr13:39980400-39983600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr13:39980400-39983800	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr13:39980400-39984400	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr13:39980800-39984600	Weak transcription	HSMM	muscle
28	chr13:39981000-39983400	Enhancers	Left Ventricle	heart
29	chr13:39981400-39991800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr13:39981400-39991800	Weak transcription	NHEK	skin
31	chr13:39981600-39983600	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr13:39981600-39983600	Weak transcription	HUVEC	blood vessel
33	chr13:39981600-39984200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr13:39981600-39985200	Weak transcription	Ovary	ovary
35	chr13:39981800-39983600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr13:39981800-39983600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr13:39981800-39988600	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr13:39982000-39986600	Enhancers	Fetal Heart	heart
39	chr13:39982400-39985200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr13:39982600-39983600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr13:39982600-39983600	Weak transcription	Brain Cingulate Gyrus	brain
42	chr13:39982800-39983800	Weak transcription	Brain Substantia Nigra	brain
43	chr13:39983000-39983200	Weak transcription	Adipose Nuclei	Adipose
44	chr13:39983000-39985000	Enhancers	Right Ventricle	heart

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