Variant report

Variant	rs3971192
Chromosome Location	chr3:151047828-151047829
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1125541	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11708287	0.89[JPT][hapmap]
rs11715892	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11717634	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12487835	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12492699	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12494865	0.90[CEU][hapmap]
rs13088531	0.83[EUR][1000 genomes]
rs13090321	0.83[EUR][1000 genomes]
rs1352886	0.84[CEU][hapmap]
rs1388627	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1388628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16863323	0.90[CEU][hapmap]
rs16863334	0.84[CEU][hapmap]
rs16863336	0.84[CEU][hapmap]
rs17204376	1.00[ASW][hapmap]
rs4076581	0.85[CEU][hapmap]
rs41399847	0.82[JPT][hapmap]
rs4679794	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6793061	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460894	chr3:150770614-151095093	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv592045	chr3:150770614-151095093	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv2754555	chr3:150968302-151054302	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv829757	chr3:151044880-151226442	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3971192	GPR171	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:151045600-151056600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr3:151045600-151063600	Weak transcription	Brain Angular Gyrus	brain
3	chr3:151046800-151048200	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr3:151046800-151049000	Weak transcription	Right Atrium	heart
5	chr3:151047000-151048200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr3:151047000-151055200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr3:151047400-151048000	Enhancers	Primary neutrophils fromperipheralblood	blood
8	chr3:151047400-151048000	Active TSS	Primary B cells from cord blood	blood
9	chr3:151047400-151050200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
10	chr3:151047600-151049800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr3:151047800-151048000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
12	chr3:151047800-151048400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr3:151047800-151049000	Active TSS	Primary hematopoietic stem cells	blood
14	chr3:151047800-151050000	Enhancers	Adipose Nuclei	Adipose

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