Variant report

Variant	rs13075534
Chromosome Location	chr3:159486139-159486140
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RP11-432B6.3.1-2	chr3:159486093-159486243	ENSG00000241211.1
2	lnc-RP11-432B6.3.1-2	chr3:159486106-159486288	ENSG00000241211.1
3	lnc-RP11-432B6.3.1-2	chr3:159486093-159486288	NONHSAT092962

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs12629172	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12631468	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13064339	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13065938	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes]
rs13065987	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13066040	0.89[MEX][hapmap]
rs13066560	1.00[CEU][hapmap];0.92[CHB][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13067050	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13072356	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13077427	0.85[CEU][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs13078322	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13080307	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13080768	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13085339	0.91[CEU][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13088481	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13088959	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13100094	0.85[CEU][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs13100614	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16830741	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16830748	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16830780	0.85[CEU][hapmap]
rs2076889	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.92[GIH][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2126142	0.85[CEU][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs2366405	0.85[CEU][hapmap]
rs34586932	0.92[ASN][1000 genomes]
rs34682429	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35035161	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35165740	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35527279	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35792854	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3892994	0.91[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4680522	0.91[ASN][1000 genomes]
rs56077320	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58755984	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61597037	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441272	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs6792870	0.85[CEU][hapmap];0.89[MEX][hapmap]
rs71625413	0.97[AMR][1000 genomes]
rs7631400	0.85[CEU][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs9860588	0.85[CEU][hapmap]
rs9880487	0.85[CEU][hapmap];0.89[MEX][hapmap]
rs9884085	0.85[CEU][hapmap];0.89[MEX][hapmap]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13075534	PUS3	trans	parietal	SCAN

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:159483600-159493000	Weak transcription	Gastric	stomach
2	chr3:159483800-159488000	Weak transcription	Spleen	Spleen
3	chr3:159483800-159493200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:159484000-159488200	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr3:159484000-159494600	Weak transcription	Psoas Muscle	Psoas
6	chr3:159484200-159486400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:159484200-159493200	Weak transcription	Lung	lung
8	chr3:159484200-159501200	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr3:159484400-159486800	Enhancers	Fetal Heart	heart
10	chr3:159484400-159488000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr3:159484400-159493000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr3:159484400-159493000	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr3:159484400-159493000	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr3:159484400-159493200	Weak transcription	Fetal Stomach	stomach
15	chr3:159484400-159505400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr3:159484600-159487200	Weak transcription	Fetal Intestine Large	intestine
17	chr3:159484600-159500400	Weak transcription	Fetal Intestine Small	intestine
18	chr3:159484800-159488400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr3:159484800-159489800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr3:159484800-159493000	Weak transcription	HSMMtube	muscle
21	chr3:159485000-159486200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr3:159485000-159486800	Enhancers	Brain Substantia Nigra	brain
23	chr3:159485000-159486800	Enhancers	Rectal Smooth Muscle	rectum
24	chr3:159485000-159486800	Strong transcription	NHEK	skin
25	chr3:159485000-159488200	Weak transcription	Brain Anterior Caudate	brain
26	chr3:159485000-159492600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr3:159485000-159492800	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr3:159485000-159493000	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr3:159485200-159486200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr3:159485200-159486400	Weak transcription	NHLF	lung
31	chr3:159485400-159486400	Enhancers	HUVEC	blood vessel
32	chr3:159485400-159486600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr3:159485400-159486800	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
34	chr3:159485400-159486800	Enhancers	NHDF-Ad	bronchial
35	chr3:159485400-159488400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr3:159485600-159486200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr3:159485600-159486200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr3:159485600-159486200	Enhancers	Colon Smooth Muscle	Colon
39	chr3:159485600-159486400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr3:159485600-159486400	Weak transcription	Left Ventricle	heart
41	chr3:159485600-159486400	Genic enhancers	NH-A	brain
42	chr3:159485600-159486800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
43	chr3:159485600-159489600	Weak transcription	Aorta	Aorta
44	chr3:159485600-159493000	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr3:159485600-159493000	Weak transcription	HMEC	breast
46	chr3:159485600-159493400	Weak transcription	Fetal Brain Female	brain
47	chr3:159485800-159486200	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr3:159485800-159486200	Strong transcription	HSMM	muscle
49	chr3:159485800-159486400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr3:159485800-159486400	Enhancers	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links