Variant report

Variant	rs840772
Chromosome Location	chr12:44734268-44734269
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10506245	0.83[ASN][1000 genomes]
rs10736020	0.84[AFR][1000 genomes]
rs1098497	0.83[ASN][1000 genomes]
rs11182497	0.90[EUR][1000 genomes]
rs11182501	0.89[EUR][1000 genomes]
rs11611818	0.86[EUR][1000 genomes]
rs12308701	0.88[EUR][1000 genomes]
rs12310262	0.90[EUR][1000 genomes]
rs1493755	0.99[EUR][1000 genomes]
rs1527315	0.83[ASN][1000 genomes]
rs1622682	1.00[CHD][hapmap];0.83[ASN][1000 genomes]
rs1625442	1.00[CHD][hapmap];0.83[ASN][1000 genomes]
rs1643432	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]
rs1643433	0.83[ASN][1000 genomes]
rs1643434	0.87[YRI][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1644007	1.00[CHD][hapmap];0.83[ASN][1000 genomes]
rs1644014	1.00[CHD][hapmap];0.83[ASN][1000 genomes]
rs1716605	0.83[ASN][1000 genomes]
rs1716606	0.83[ASN][1000 genomes]
rs1726879	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1726884	0.83[ASN][1000 genomes]
rs1726887	1.00[CHD][hapmap];0.83[ASN][1000 genomes]
rs1726888	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1726889	0.83[ASN][1000 genomes]
rs1726890	0.83[ASN][1000 genomes]
rs1726900	0.83[ASN][1000 genomes]
rs1798020	1.00[CHD][hapmap];0.83[ASN][1000 genomes]
rs1798023	0.83[ASN][1000 genomes]
rs1798027	1.00[CHD][hapmap]
rs1798033	0.83[ASN][1000 genomes]
rs1873981	0.91[EUR][1000 genomes]
rs58802461	0.83[ASN][1000 genomes]
rs60441308	0.83[ASN][1000 genomes]
rs68107418	0.90[EUR][1000 genomes]
rs7132743	0.86[EUR][1000 genomes]
rs7300557	0.81[YRI][hapmap];0.84[AFR][1000 genomes]
rs73276236	0.83[ASN][1000 genomes]
rs73276240	0.83[ASN][1000 genomes]
rs73276275	0.83[ASN][1000 genomes]
rs7958975	0.83[ASN][1000 genomes]
rs7961768	0.85[EUR][1000 genomes]
rs7974460	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs840764	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs840766	0.83[ASN][1000 genomes]
rs840767	0.83[ASN][1000 genomes]
rs840768	0.83[ASN][1000 genomes]
rs840773	0.83[ASN][1000 genomes]
rs840774	0.83[ASN][1000 genomes]
rs859016	0.83[ASN][1000 genomes]
rs863482	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	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	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
3	nsv826356	chr12:44725069-44783443	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs840772	SRSF2IP	cis	cerebellum	SCAN
rs840772	PUS7L	cis	cerebellum	SCAN
rs840772	NDN	trans	lymphoblastoid	seeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:44699000-44736000	Weak transcription	Pancreas	Pancrea
2	chr12:44699000-44782000	Weak transcription	Aorta	Aorta
3	chr12:44709200-44743200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr12:44712400-44765800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr12:44728400-44744800	Weak transcription	Esophagus	oesophagus
6	chr12:44732400-44735600	Weak transcription	Ovary	ovary
7	chr12:44732800-44736000	Weak transcription	Stomach Smooth Muscle	stomach
8	chr12:44733800-44736000	Weak transcription	Fetal Intestine Small	intestine
9	chr12:44734000-44734800	Enhancers	Fetal Brain Female	brain
10	chr12:44734000-44734800	Enhancers	Rectal Smooth Muscle	rectum
11	chr12:44734200-44734800	Enhancers	Fetal Brain Male	brain
12	chr12:44734200-44736400	Enhancers	Colon Smooth Muscle	Colon

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