Variant report

Variant	rs2972549
Chromosome Location	chr19:36749658-36749659
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10402043	0.82[CHB][hapmap]
rs10409091	0.90[CHB][hapmap]
rs10418510	0.87[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap]
rs10420071	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs2070132	0.95[CHB][hapmap];0.91[CHD][hapmap];0.82[JPT][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap]
rs2271844	0.87[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap]
rs2287897	0.90[CHB][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap]
rs2287898	0.90[CHB][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap]
rs2310856	0.81[ASN][1000 genomes]
rs2385801	0.87[CEU][hapmap];0.82[CHD][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap]
rs2385803	0.87[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs2385804	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2432039	0.95[CHB][hapmap]
rs2432045	0.95[CHB][hapmap];0.83[CHD][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap]
rs2432049	0.95[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs2432052	0.84[LWK][hapmap];0.81[ASN][1000 genomes]
rs2432054	0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];0.87[LWK][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];0.87[TSI][hapmap];0.81[ASN][1000 genomes]
rs2438514	0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];0.91[LWK][hapmap];0.90[MEX][hapmap];0.86[MKK][hapmap];0.87[TSI][hapmap]
rs2438517	0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];0.87[TSI][hapmap];0.81[ASN][1000 genomes]
rs2918332	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2918337	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2918338	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2918357	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2918375	0.81[ASN][1000 genomes]
rs2918379	0.82[ASN][1000 genomes]
rs2918380	0.82[ASN][1000 genomes]
rs2945945	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap]
rs2945950	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2945961	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap]
rs2945972	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap]
rs2945985	0.87[CEU][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap]
rs2945993	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap]
rs2967484	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap]
rs2967504	0.87[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap]
rs2967506	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap]
rs2967517	0.87[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap]
rs2967518	0.87[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap]
rs2967521	0.83[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap]
rs2967524	0.87[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap]
rs2967526	0.87[CEU][hapmap]
rs2972321	0.81[ASN][1000 genomes]
rs2972525	0.94[ASN][1000 genomes]
rs2972526	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2972529	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2972537	0.82[ASN][1000 genomes]
rs2972539	0.82[ASN][1000 genomes]
rs2972544	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4239585	0.95[CHB][hapmap]
rs7246106	0.87[CEU][hapmap]
rs7253462	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7507379	0.87[ASN][1000 genomes]
rs8102020	0.90[CHB][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2972549	LOC284412	N/A	lymphoblastoid	RTeQTL
rs2972549	LINC00665	cis	Artery Tibial	GTEx
rs2972549	ZNF545	cis	multi-tissue	Pritchard
rs2972549	KIAA1559	cis	multi-tissue	Pritchard

Chromatin state (count:16 , 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	chr19:36747800-36749800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr19:36747800-36749800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr19:36748800-36762800	Weak transcription	Right Atrium	heart
7	chr19:36749200-36762800	Weak transcription	Colon Smooth Muscle	Colon
8	chr19:36749200-36764800	Weak transcription	Brain Substantia Nigra	brain
9	chr19:36749400-36749800	Enhancers	Brain Anterior Caudate	brain
10	chr19:36749400-36749800	Enhancers	Brain Cingulate Gyrus	brain
11	chr19:36749400-36762600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr19:36749400-36764200	Weak transcription	Brain Angular Gyrus	brain
13	chr19:36749600-36750200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr19:36749600-36757400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr19:36749600-36762600	Weak transcription	Brain Hippocampus Middle	brain
16	chr19:36749600-36763400	Weak transcription	Brain Inferior Temporal Lobe	brain

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