Variant report

Variant	rs2119787
Chromosome Location	chr4:90734728-90734729
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10009760	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];0.83[TSI][hapmap];0.92[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10030935	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10155475	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1023777	0.82[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.90[MKK][hapmap];0.80[TSI][hapmap];0.92[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11097234	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11097238	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12502363	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12649704	0.84[ASN][1000 genomes]
rs2736990	0.80[JPT][hapmap]
rs2870028	0.96[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs356168	0.80[JPT][hapmap]
rs356200	0.80[JPT][hapmap]
rs356204	0.80[JPT][hapmap]
rs3796664	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3796665	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3822095	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3910104	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3910105	0.92[AFR][1000 genomes]
rs6848726	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7356228	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7356297	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs765517	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7678651	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7697570	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[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	esv2830400	chr4:90085456-90922432	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv1012406	chr4:90167781-91166787	Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv949454	chr4:90272120-91156917	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv879536	chr4:90678541-90775212	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2119787	FAM190A	cis	cerebellum	SCAN
rs2119787	DSPP	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:90709800-90735400	Weak transcription	Ovary	ovary
2	chr4:90714800-90740400	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr4:90718800-90748000	Weak transcription	Brain Angular Gyrus	brain
4	chr4:90719000-90747600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr4:90722200-90751800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr4:90722400-90741200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr4:90722600-90741400	Weak transcription	HMEC	breast
8	chr4:90723000-90741400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr4:90725600-90735400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr4:90727000-90743200	Weak transcription	Fetal Lung	lung
11	chr4:90729000-90741600	Weak transcription	NHEK	skin
12	chr4:90730200-90757200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr4:90730800-90757000	Weak transcription	Fetal Stomach	stomach
14	chr4:90731600-90743000	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr4:90732600-90734800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr4:90732600-90741200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr4:90733800-90734800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr4:90734000-90736400	Strong transcription	Primary hematopoietic stem cells	blood
19	chr4:90734000-90736600	Strong transcription	Dnd41	blood
20	chr4:90734200-90739400	Weak transcription	HUVEC	blood vessel
21	chr4:90734400-90735400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr4:90734600-90734800	Enhancers	H9 Cell Line	embryonic stem cell
23	chr4:90734600-90743000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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