Variant report

Variant	rs2972548
Chromosome Location	chr19:36749804-36749805
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10418925	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs11084857	0.85[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.88[TSI][hapmap]
rs1127406	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap]
rs1129375	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]
rs1129376	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.95[TSI][hapmap]
rs11672641	0.99[ASN][1000 genomes]
rs11882601	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]
rs12460237	0.91[CHB][hapmap]
rs12609058	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]
rs17206365	1.00[CEU][hapmap]
rs17639740	0.88[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]
rs1898675	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2432048	0.90[CHB][hapmap]
rs2432053	0.84[CEU][hapmap];0.91[CHB][hapmap];0.90[TSI][hapmap]
rs2432055	0.91[CHB][hapmap]
rs2910681	0.91[CHB][hapmap]
rs2918322	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2918323	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2918324	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2918325	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.82[LWK][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2918328	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2918329	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2918330	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2918331	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2918334	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2918355	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2918356	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2918358	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2918377	0.91[CHB][hapmap]
rs2918382	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2918383	0.81[AMR][1000 genomes]
rs2918384	0.88[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2967490	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap]
rs2967491	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap]
rs2972320	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2972528	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2972530	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2972532	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2972533	0.88[CEU][hapmap];0.91[CHB][hapmap];0.80[CHD][hapmap];0.90[JPT][hapmap];0.80[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2972534	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2972536	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2972540	0.84[CEU][hapmap];0.81[CHB][hapmap];0.90[TSI][hapmap]
rs2972545	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2972550	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2972551	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2972554	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2972630	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2972631	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2972643	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]
rs2972654	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]
rs2972655	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4805169	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4805170	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4806289	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4806291	0.99[ASN][1000 genomes]
rs4806292	0.91[EUR][1000 genomes]
rs6510528	0.86[CHB][hapmap]
rs7254149	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7255170	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9797716	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520020	chr19:36721368-36822594	Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv9715	chr19:36729688-36811749	Weak transcription Active TSS Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1063208	chr19:36743461-36847486	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv961212	chr19:36744378-36801298	ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv960831	chr19:36744378-36813769	Weak transcription Active TSS Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1056901	chr19:36749658-36847486	Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv511620	chr19:36749804-36801902	Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv579426	chr19:36749804-36802219	Weak transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2972548	SERTAD1	cis	cerebellum	SCAN
rs2972548	GGN	cis	cerebellum	SCAN
rs2972548	ZNF383	cis	cerebellum	SCAN
rs2972548	ZFP82	cis	lymphoblastoid	seeQTL
rs2972548	DPF1	cis	cerebellum	SCAN
rs2972548	ZNF545	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36739600-36756800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr19:36745800-36750600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
3	chr19:36747000-36750000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr19:36748800-36762800	Weak transcription	Right Atrium	heart
5	chr19:36749200-36762800	Weak transcription	Colon Smooth Muscle	Colon
6	chr19:36749200-36764800	Weak transcription	Brain Substantia Nigra	brain
7	chr19:36749400-36762600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr19:36749400-36764200	Weak transcription	Brain Angular Gyrus	brain
9	chr19:36749600-36750200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr19:36749600-36757400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr19:36749600-36762600	Weak transcription	Brain Hippocampus Middle	brain
12	chr19:36749600-36763400	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr19:36749800-36757600	Weak transcription	Brain Anterior Caudate	brain
14	chr19:36749800-36760000	Weak transcription	Brain Cingulate Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links