Variant report

Variant	rs2025328
Chromosome Location	chr9:21531637-21531638
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10120766	0.91[ASN][1000 genomes]
rs10124767	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10491566	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10757222	0.81[CEU][hapmap]
rs10965025	0.87[CEU][hapmap]
rs10965026	0.80[CEU][hapmap]
rs10965048	0.84[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1332181	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1412395	0.81[CEU][hapmap]
rs1591035	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2025327	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2026983	0.81[CEU][hapmap]
rs2039378	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2039379	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2146797	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2183904	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2210437	0.85[CHB][hapmap];0.87[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.81[TSI][hapmap];0.83[ASN][1000 genomes]
rs2383193	0.88[CEU][hapmap]
rs2383194	0.87[CEU][hapmap]
rs6475538	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs720975	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs725074	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7863623	0.85[ASN][1000 genomes]
rs7868724	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][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	nsv892740	chr9:21471499-21551513	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA miRNA	110 gene(s)	inside rSNPs	diseases
2	nsv1031432	chr9:21472601-21608774	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	122 gene(s)	inside rSNPs	diseases
3	nsv540085	chr9:21472601-21608774	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	122 gene(s)	inside rSNPs	diseases
4	nsv892741	chr9:21517302-21551513	Genic enhancers Enhancers Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2025328	IFNB1	cis	parietal	SCAN
rs2025328	PTPLAD2	cis	parietal	SCAN
rs2025328	RPS6	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21507200-21551400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr9:21508000-21542000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr9:21516800-21542600	Weak transcription	Stomach Mucosa	stomach
4	chr9:21522600-21532600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr9:21522600-21533200	Strong transcription	NH-A	brain
6	chr9:21524400-21532200	Strong transcription	Osteobl	bone
7	chr9:21525600-21534000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr9:21526200-21532400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr9:21526400-21534800	Strong transcription	NHEK	skin
10	chr9:21526600-21533000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr9:21526800-21534800	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr9:21527800-21536600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr9:21528200-21532800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr9:21528600-21531800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr9:21528800-21532200	Strong transcription	HMEC	breast
16	chr9:21528800-21533000	Strong transcription	Hela-S3	cervix
17	chr9:21528800-21533400	Weak transcription	Fetal Intestine Large	intestine
18	chr9:21528800-21535800	Weak transcription	Gastric	stomach
19	chr9:21528800-21542000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr9:21529000-21532000	Weak transcription	HUVEC	blood vessel
21	chr9:21529000-21533200	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr9:21529000-21534800	Weak transcription	Esophagus	oesophagus
23	chr9:21529000-21551400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr9:21530000-21532000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr9:21530000-21532000	Strong transcription	A549	lung
26	chr9:21530200-21531800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr9:21530200-21533600	Weak transcription	HSMM	muscle
28	chr9:21530400-21532400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr9:21530800-21533200	Genic enhancers	Muscle Satellite Cultured Cells	--
30	chr9:21530800-21533400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr9:21530800-21535000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr9:21531000-21531800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr9:21531000-21533600	Weak transcription	NHDF-Ad	bronchial
34	chr9:21531400-21532200	Strong transcription	NHLF	lung
35	chr9:21531600-21542600	Weak transcription	Duodenum Mucosa	Duodenum

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