Variant report

Variant	rs1643432
Chromosome Location	chr12:44693945-44693946
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10506245	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10736020	0.92[YRI][hapmap]
rs1098497	1.00[ASN][1000 genomes]
rs1493755	0.82[EUR][1000 genomes]
rs1527315	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1622682	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs1625442	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs1643433	1.00[ASN][1000 genomes]
rs1643434	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1644007	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs1644009	0.83[ASN][1000 genomes]
rs1644010	0.83[ASN][1000 genomes]
rs1644011	0.83[ASN][1000 genomes]
rs1644012	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1644014	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs1716605	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1716606	1.00[ASN][1000 genomes]
rs1716609	1.00[CHB][hapmap]
rs1726874	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs1726879	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1726884	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1726887	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs1726888	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1726889	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1726890	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1726900	1.00[ASN][1000 genomes]
rs1798020	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs1798023	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1798025	0.83[ASN][1000 genomes]
rs1798026	0.83[ASN][1000 genomes]
rs1798027	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[ASN][1000 genomes]
rs1798032	1.00[CHB][hapmap]
rs58802461	1.00[ASN][1000 genomes]
rs60441308	1.00[ASN][1000 genomes]
rs7300557	0.89[YRI][hapmap]
rs7314412	1.00[CHB][hapmap]
rs73274199	0.83[ASN][1000 genomes]
rs73276236	1.00[ASN][1000 genomes]
rs73276240	1.00[ASN][1000 genomes]
rs73276275	1.00[ASN][1000 genomes]
rs7958975	1.00[ASN][1000 genomes]
rs7974460	1.00[CHD][hapmap]
rs840764	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs840766	1.00[ASN][1000 genomes]
rs840767	1.00[ASN][1000 genomes]
rs840768	1.00[ASN][1000 genomes]
rs840772	0.94[ASW][hapmap];0.87[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];0.85[MEX][hapmap];0.99[MKK][hapmap];0.96[TSI][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs840773	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs840774	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs859016	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs863482	1.00[CHB][hapmap];1.00[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	nsv1049818	chr12:44486312-45133783	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv686	chr12:44671240-44696910	Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription	lncRNA	n/a	inside rSNPs	n/a
3	nsv1038498	chr12:44679455-44816572	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1643432	PUS7L	cis	cerebellum	SCAN
rs1643432	SRSF2IP	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:44676600-44697800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr12:44682000-44698600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr12:44685000-44695400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr12:44688800-44702000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr12:44690400-44697800	Weak transcription	HSMMtube	muscle
6	chr12:44690400-44698000	Weak transcription	Liver	Liver
7	chr12:44690400-44698600	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr12:44690600-44697800	Weak transcription	Aorta	Aorta
9	chr12:44690600-44697800	Weak transcription	Duodenum Mucosa	Duodenum
10	chr12:44690800-44694800	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr12:44690800-44696000	Weak transcription	Pancreas	Pancrea
12	chr12:44690800-44698000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr12:44690800-44698000	Weak transcription	Esophagus	oesophagus
14	chr12:44690800-44701400	Weak transcription	Left Ventricle	heart
15	chr12:44691400-44701400	Weak transcription	Psoas Muscle	Psoas
16	chr12:44693200-44694200	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr12:44693200-44694200	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr12:44693200-44694200	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr12:44693200-44694200	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr12:44693200-44694200	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr12:44693200-44694400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr12:44693400-44694400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr12:44693600-44694000	Enhancers	H1 Cell Line	embryonic stem cell
24	chr12:44693600-44694400	Enhancers	Fetal Brain Male	brain
25	chr12:44693600-44697800	Weak transcription	Fetal Intestine Small	intestine
26	chr12:44693600-44698600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links