Variant report

Variant	rs1409597
Chromosome Location	chr12:87563845-87563846
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MGAT4C-4	chr12:87563762-87564206	NONHSAT029769

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10777016	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10777017	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10777020	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10858550	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10858551	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10858552	0.81[AMR][1000 genomes]
rs10858555	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10858557	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10858560	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11104240	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11104255	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11104276	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11104287	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11104288	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11104289	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11104290	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11104291	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11104292	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11104293	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11104294	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11104301	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11104305	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11104306	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11104327	0.81[AFR][1000 genomes]
rs12227528	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12231093	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12308273	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12310504	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12311381	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12422524	0.86[AMR][1000 genomes]
rs12425011	0.85[AMR][1000 genomes]
rs12425030	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12813510	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12813826	0.86[AMR][1000 genomes]
rs1326736	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1344794	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1344795	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1347217	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1368563	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1368564	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1409596	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1433328	0.83[AMR][1000 genomes]
rs1433329	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1433330	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1433331	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1433333	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1583313	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17314381	0.86[AMR][1000 genomes]
rs1882660	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1897631	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1897633	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2053090	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2053091	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2053092	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2117015	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2117016	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2897503	0.86[AMR][1000 genomes]
rs4842543	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs67092872	0.86[AMR][1000 genomes]
rs67550411	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7134010	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7137108	0.86[ASN][1000 genomes]
rs7138714	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7139356	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7316038	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7487188	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7954553	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7964342	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7967533	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7969732	0.86[AMR][1000 genomes]
rs7970360	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7971422	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7974893	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2754127	chr12:86723232-87576932	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv916862	chr12:86837694-87718558	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv899397	chr12:86863041-87636831	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv868879	chr12:87207243-87578373	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1052693	chr12:87219949-87573582	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv899416	chr12:87442480-87588533	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv899417	chr12:87475632-87588533	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv1036043	chr12:87503257-87592799	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv1054581	chr12:87510821-87669648	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv976644	chr12:87563287-87563955	Weak transcription ZNF genes & repeats Enhancers	lncRNA	n/a	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:87563800-87564000	ZNF genes & repeats	Aorta	Aorta
2	chr12:87563800-87564000	Enhancers	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links