Variant report

Variant	rs1425286
Chromosome Location	chr9:79229024-79229025
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RFK-5	chr9:79228924-79229516	NONHSAT131960

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10512062	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11144974	0.84[AFR][1000 genomes]
rs11144975	0.84[AFR][1000 genomes]
rs1329020	1.00[CEU][hapmap]
rs1425285	0.91[EUR][1000 genomes]
rs1536821	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs3174372	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3174373	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs700804	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs700806	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs700808	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs700809	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs7028529	0.91[EUR][1000 genomes]
rs7042069	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7046144	1.00[CEU][hapmap]
rs707741	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs73650263	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7865889	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869152	chr9:78742197-79583399	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv931033	chr9:78850330-79366454	Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv893479	chr9:78971253-79275226	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv949417	chr9:79078703-79282589	Strong transcription Genic enhancers Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv527438	chr9:79225328-79230242	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:79211000-79229200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr9:79215400-79229400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr9:79221000-79229400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr9:79221200-79229800	Weak transcription	GM12878-XiMat	blood
5	chr9:79223600-79229400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr9:79223600-79230200	Weak transcription	Primary B cells from cord blood	blood
7	chr9:79224400-79229600	Enhancers	Stomach Mucosa	stomach
8	chr9:79224600-79239000	Weak transcription	Brain Cingulate Gyrus	brain
9	chr9:79224600-79244400	Weak transcription	Brain Angular Gyrus	brain
10	chr9:79224800-79239600	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr9:79225200-79239000	Weak transcription	Brain Anterior Caudate	brain
12	chr9:79225200-79239600	Weak transcription	Brain Substantia Nigra	brain
13	chr9:79225400-79233600	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr9:79225400-79233600	Weak transcription	Stomach Smooth Muscle	stomach
15	chr9:79225400-79239200	Weak transcription	Colon Smooth Muscle	Colon
16	chr9:79225400-79244000	Weak transcription	Brain Hippocampus Middle	brain
17	chr9:79225400-79265600	Weak transcription	Fetal Muscle Leg	muscle
18	chr9:79225600-79229200	Weak transcription	Fetal Lung	lung
19	chr9:79225600-79229200	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr9:79225600-79229600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr9:79225600-79229800	Weak transcription	Osteobl	bone
22	chr9:79225600-79232400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr9:79225600-79233400	Weak transcription	HSMMtube	muscle
24	chr9:79225800-79229600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr9:79225800-79232200	Weak transcription	Gastric	stomach
26	chr9:79225800-79232600	Weak transcription	Rectal Smooth Muscle	rectum
27	chr9:79225800-79234000	Weak transcription	HSMM	muscle
28	chr9:79227200-79229400	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr9:79227400-79229400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr9:79228000-79234000	Weak transcription	Aorta	Aorta
31	chr9:79228200-79229800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr9:79228400-79230000	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr9:79228600-79230200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr9:79228800-79229400	Enhancers	Fetal Intestine Large	intestine
35	chr9:79228800-79229400	Enhancers	Fetal Intestine Small	intestine
36	chr9:79228800-79229600	Active TSS	Duodenum Mucosa	Duodenum
37	chr9:79228800-79230000	Enhancers	Rectal Mucosa Donor 29	rectum
38	chr9:79228800-79230200	Enhancers	Primary monocytes fromperipheralblood	blood
39	chr9:79228800-79230800	Enhancers	HepG2	liver
40	chr9:79229000-79230200	Enhancers	Primary hematopoietic stem cells	blood
41	chr9:79229000-79230200	Enhancers	Rectal Mucosa Donor 31	rectum

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