Variant report

Variant	rs1398525
Chromosome Location	chr3:145894098-145894099
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1170389	0.84[JPT][hapmap]
rs12485283	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs13088646	1.00[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1707469	0.80[GIH][hapmap]
rs17414130	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1913186	1.00[CEU][hapmap];0.89[GIH][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2137485	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2175668	0.84[ASW][hapmap];0.96[LWK][hapmap];0.89[MKK][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes]
rs2203213	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34800183	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4342076	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6766101	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7623263	1.00[CEU][hapmap];0.89[CHB][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7625569	0.93[AFR][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	nsv877613	chr3:145833232-145912055	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv1011146	chr3:145859022-145911429	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv1012485	chr3:145861750-145947125	Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv536758	chr3:145861750-145947125	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1398525	HLTF	cis	parietal	SCAN
rs1398525	PLSCR1	cis	parietal	SCAN
rs1398525	CPA3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:145880800-145914400	Weak transcription	Left Ventricle	heart
2	chr3:145883000-145913000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr3:145884000-145903400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr3:145884800-145910800	Weak transcription	Liver	Liver
5	chr3:145885000-145908000	Weak transcription	Aorta	Aorta
6	chr3:145885400-145895400	Weak transcription	HSMM	muscle
7	chr3:145885600-145907800	Weak transcription	Ovary	ovary
8	chr3:145888600-145902000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr3:145891000-145894600	Weak transcription	A549	lung
10	chr3:145891000-145895200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr3:145891200-145894800	Weak transcription	Osteobl	bone
12	chr3:145892600-145895600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr3:145892800-145896400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr3:145893400-145894800	Enhancers	HUVEC	blood vessel

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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