Variant report

Variant	rs1812923
Chromosome Location	chr4:90739539-90739540
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10005233	0.85[CEU][hapmap]
rs1442143	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[MKK][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1442145	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1471483	0.81[CEU][hapmap]
rs1837890	0.88[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.85[LWK][hapmap];0.90[MKK][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2583960	0.85[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2619372	0.88[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.85[LWK][hapmap];0.90[MKK][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2737020	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6532191	0.85[CEU][hapmap]
rs7681440	0.81[CEU][hapmap]
rs972880	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs974711	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1812923	FAM190A	cis	cerebellum	SCAN
rs1812923	DSPP	cis	cerebellum	SCAN
rs1812923	DSPP	cis	parietal	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:90714800-90740400	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr4:90718800-90748000	Weak transcription	Brain Angular Gyrus	brain
3	chr4:90719000-90747600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr4:90722200-90751800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr4:90722400-90741200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr4:90722600-90741400	Weak transcription	HMEC	breast
7	chr4:90723000-90741400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr4:90727000-90743200	Weak transcription	Fetal Lung	lung
9	chr4:90729000-90741600	Weak transcription	NHEK	skin
10	chr4:90730200-90757200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr4:90730800-90757000	Weak transcription	Fetal Stomach	stomach
12	chr4:90731600-90743000	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr4:90732600-90741200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr4:90734600-90743000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr4:90734800-90739600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr4:90734800-90740800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr4:90734800-90750600	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr4:90735400-90749600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr4:90735800-90741200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr4:90735800-90755600	Weak transcription	Fetal Brain Male	brain
21	chr4:90736000-90743200	Weak transcription	Ovary	ovary
22	chr4:90736200-90750600	Weak transcription	Fetal Thymus	thymus
23	chr4:90736400-90739800	Weak transcription	Primary hematopoietic stem cells	blood
24	chr4:90736600-90739600	Weak transcription	Dnd41	blood
25	chr4:90737400-90740200	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr4:90738000-90750800	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr4:90738000-90755800	Weak transcription	Fetal Brain Female	brain
28	chr4:90738200-90750400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr4:90738200-90750800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr4:90738400-90745400	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr4:90738400-90750400	Weak transcription	Brain Anterior Caudate	brain
32	chr4:90738400-90750600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr4:90738400-90756600	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr4:90739400-90739600	Enhancers	Brain Hippocampus Middle	brain
35	chr4:90739400-90743800	Genic enhancers	HUVEC	blood vessel

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