Variant report

Variant	rs9506288
Chromosome Location	chr13:30880032-30880033
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12873373	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1952607	0.84[YRI][hapmap]
rs35962246	0.91[ASN][1000 genomes]
rs4769824	0.96[CEU][hapmap];0.96[EUR][1000 genomes]
rs6490453	0.96[EUR][1000 genomes]
rs7335432	0.85[EUR][1000 genomes]
rs756850	0.84[CEU][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs763808	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7991052	0.89[EUR][1000 genomes]
rs9506290	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9506291	0.85[EUR][1000 genomes]
rs9506292	0.85[EUR][1000 genomes]
rs9508700	0.96[CEU][hapmap];0.95[GIH][hapmap];0.98[TSI][hapmap];0.95[EUR][1000 genomes]
rs9508701	0.93[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9508702	0.95[CEU][hapmap];0.95[EUR][1000 genomes]
rs9508703	0.96[CEU][hapmap];0.93[GIH][hapmap];0.98[TSI][hapmap];0.95[EUR][1000 genomes]
rs9508705	0.85[EUR][1000 genomes]
rs9508706	0.85[EUR][1000 genomes]
rs9508711	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9551887	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9634361	0.89[EUR][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9506288	POLR1D	cis	parietal	SCAN
rs9506288	KATNAL1	cis	cerebellum	SCAN
rs9506288	FLT3	cis	parietal	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30843000-30880200	Weak transcription	Fetal Stomach	stomach
2	chr13:30861000-30880800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr13:30866800-30880800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr13:30868400-30880800	Weak transcription	Left Ventricle	heart
5	chr13:30870800-30880400	Weak transcription	Fetal Muscle Trunk	muscle
6	chr13:30871000-30880400	Weak transcription	Fetal Intestine Small	intestine
7	chr13:30871000-30880400	Weak transcription	Right Ventricle	heart
8	chr13:30876000-30880600	Enhancers	Fetal Brain Male	brain
9	chr13:30876200-30880400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr13:30876200-30880600	Weak transcription	Ovary	ovary
11	chr13:30876400-30880800	Weak transcription	Lung	lung
12	chr13:30876600-30880600	Enhancers	Fetal Heart	heart
13	chr13:30876800-30880200	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr13:30877000-30880600	Enhancers	Primary B cells from cord blood	blood
15	chr13:30877200-30880400	Enhancers	HepG2	liver
16	chr13:30877200-30880600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
17	chr13:30877400-30880600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr13:30877400-30880600	Enhancers	Primary B cells from peripheral blood	blood
19	chr13:30877800-30880400	Flanking Active TSS	Dnd41	blood
20	chr13:30877800-30880800	Weak transcription	Spleen	Spleen
21	chr13:30878000-30880200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr13:30878000-30880200	Enhancers	K562	blood
23	chr13:30878000-30880600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr13:30878000-30880600	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr13:30878200-30880400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr13:30878200-30880600	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr13:30878400-30880600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr13:30878800-30880400	Enhancers	Brain Anterior Caudate	brain
29	chr13:30878800-30880600	Weak transcription	Brain Hippocampus Middle	brain
30	chr13:30878800-30880800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr13:30879000-30880400	Enhancers	Rectal Smooth Muscle	rectum
32	chr13:30879000-30880600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr13:30879200-30880200	Flanking Active TSS	NHDF-Ad	bronchial
34	chr13:30879400-30880200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr13:30879400-30880400	Enhancers	iPS-18 Cell Line	embryonic stem cell
36	chr13:30879400-30880400	Enhancers	Fetal Lung	lung
37	chr13:30879400-30880400	Enhancers	HSMM	muscle
38	chr13:30879400-30880600	Enhancers	Brain Substantia Nigra	brain
39	chr13:30879400-30880800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr13:30879400-30881000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr13:30879600-30880200	Enhancers	H1 Cell Line	embryonic stem cell
42	chr13:30879600-30880200	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr13:30879600-30880200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
44	chr13:30879600-30880400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr13:30879600-30880400	Enhancers	Fetal Muscle Leg	muscle
46	chr13:30879600-30880400	Enhancers	Skeletal Muscle Male	skeletal muscle
47	chr13:30879600-30880600	Enhancers	Primary hematopoietic stem cells	blood
48	chr13:30879600-30880600	Enhancers	Hela-S3	cervix
49	chr13:30879600-30880600	Enhancers	HSMMtube	muscle
50	chr13:30879600-30881000	Flanking Active TSS	Adipose Nuclei	Adipose

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