Variant report

Variant	rs2972525
Chromosome Location	chr19:36747279-36747280
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10409091	0.86[CHB][hapmap]
rs10418510	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs10420071	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs2070132	1.00[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs2271844	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs2287897	0.86[CHB][hapmap]
rs2287898	0.86[CHB][hapmap]
rs2310856	0.85[ASN][1000 genomes]
rs2385803	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs2385804	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs2432039	1.00[CHB][hapmap]
rs2432042	0.83[ASN][1000 genomes]
rs2432045	1.00[CHB][hapmap]
rs2432049	1.00[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs2432052	0.85[ASN][1000 genomes]
rs2432054	1.00[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs2438514	1.00[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs2438517	1.00[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs2918325	0.88[YRI][hapmap];0.80[AFR][1000 genomes]
rs2918332	0.94[ASN][1000 genomes]
rs2918337	0.90[ASN][1000 genomes]
rs2918338	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2918357	0.94[ASN][1000 genomes]
rs2918375	0.85[ASN][1000 genomes]
rs2918379	0.86[ASN][1000 genomes]
rs2918380	0.86[ASN][1000 genomes]
rs2945945	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs2945950	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs2945961	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs2945972	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs2945993	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs2967484	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2967504	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs2967506	0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2967517	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs2967518	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs2967521	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs2967524	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs2972321	0.85[ASN][1000 genomes]
rs2972526	0.99[ASN][1000 genomes]
rs2972529	0.87[ASN][1000 genomes]
rs2972530	0.82[AFR][1000 genomes]
rs2972537	0.86[ASN][1000 genomes]
rs2972539	0.86[ASN][1000 genomes]
rs2972544	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2972549	0.94[ASN][1000 genomes]
rs4239585	1.00[CHB][hapmap]
rs7253462	0.94[ASN][1000 genomes]
rs7507379	0.83[ASN][1000 genomes]
rs8102020	0.86[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2972525	LINC00665	cis	Muscle Skeletal	GTEx
rs2972525	LINC00665	cis	Thyroid	GTEx
rs2972525	LOC284412	N/A	lymphoblastoid	RTeQTL
rs2972525	ZFP14	cis	Lymphoblastoid	GTEx

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36730400-36748400	Weak transcription	HSMMtube	muscle
2	chr19:36737400-36747800	Weak transcription	Brain Anterior Caudate	brain
3	chr19:36737400-36747800	Weak transcription	Brain Substantia Nigra	brain
4	chr19:36737400-36748000	Weak transcription	Ovary	ovary
5	chr19:36737600-36747800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr19:36737600-36747800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr19:36737600-36747800	Weak transcription	Brain Hippocampus Middle	brain
8	chr19:36738000-36747800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr19:36739600-36756800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr19:36744800-36748000	ZNF genes & repeats	Fetal Brain Female	brain
11	chr19:36745400-36748000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
12	chr19:36745400-36749200	ZNF genes & repeats	Pancreas	Pancrea
13	chr19:36745800-36750600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
14	chr19:36746200-36747400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr19:36746200-36747400	ZNF genes & repeats	Lung	lung
16	chr19:36746200-36748200	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
17	chr19:36746200-36748800	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr19:36746200-36749400	ZNF genes & repeats	Fetal Stomach	stomach
19	chr19:36746400-36747800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr19:36746400-36747800	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr19:36746400-36748800	ZNF genes & repeats	Spleen	Spleen
22	chr19:36746800-36747800	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr19:36746800-36747800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr19:36746800-36748000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr19:36746800-36748000	Weak transcription	Stomach Smooth Muscle	stomach
26	chr19:36747000-36750000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr19:36747200-36747800	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr19:36747200-36747800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr19:36747200-36747800	Weak transcription	Brain Inferior Temporal Lobe	brain

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