Variant report

Variant	rs7040154
Chromosome Location	chr9:8692558-8692559
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10122820	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10124836	0.84[EUR][1000 genomes]
rs10125358	0.93[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10977250	0.88[EUR][1000 genomes]
rs12336593	0.93[CEU][hapmap];0.87[EUR][1000 genomes]
rs12685924	0.88[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1337805	0.93[CEU][hapmap]
rs1368981	0.94[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1368982	0.94[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1415724	0.81[CEU][hapmap]
rs1434264	0.81[CEU][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1434265	0.81[CEU][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1512380	0.81[CEU][hapmap]
rs1512381	0.81[CEU][hapmap]
rs16928221	0.93[CEU][hapmap]
rs16928238	0.93[CEU][hapmap]
rs16928282	0.85[EUR][1000 genomes]
rs3817202	0.83[EUR][1000 genomes]
rs3817209	0.83[EUR][1000 genomes]
rs3817210	0.83[EUR][1000 genomes]
rs4442186	0.84[EUR][1000 genomes]
rs57325817	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59292968	0.81[EUR][1000 genomes]
rs60000844	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60499554	0.94[EUR][1000 genomes]
rs61002972	0.94[EUR][1000 genomes]
rs7021243	0.86[CEU][hapmap];0.94[EUR][1000 genomes]
rs7030931	0.81[CEU][hapmap];0.95[EUR][1000 genomes]
rs7041517	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7042493	0.95[EUR][1000 genomes]
rs7042822	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7048587	0.93[CEU][hapmap];0.95[EUR][1000 genomes]
rs72698256	0.81[EUR][1000 genomes]
rs72700351	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031472	chr9:8250901-8712547	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv1022796	chr9:8360729-9110046	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv892228	chr9:8482778-8703733	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv892232	chr9:8645448-8698875	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv892233	chr9:8645448-8702964	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv892234	chr9:8645448-8703733	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:8679800-8696400	Weak transcription	Ovary	ovary
2	chr9:8680000-8693000	Weak transcription	Fetal Brain Female	brain
3	chr9:8680000-8694800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr9:8682000-8694800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr9:8683000-8706000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr9:8683400-8696000	Weak transcription	Fetal Lung	lung
7	chr9:8683600-8693000	Weak transcription	Primary hematopoietic stem cells	blood
8	chr9:8684200-8693000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr9:8686400-8693600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr9:8690000-8693000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr9:8690000-8693000	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr9:8690400-8695000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr9:8691000-8693800	Enhancers	Brain Substantia Nigra	brain
14	chr9:8691200-8693800	Enhancers	Brain Cingulate Gyrus	brain
15	chr9:8691200-8693800	Enhancers	Brain Hippocampus Middle	brain
16	chr9:8691400-8692800	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr9:8691600-8693000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr9:8691800-8693600	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr9:8692000-8693000	Weak transcription	Brain Anterior Caudate	brain
20	chr9:8692200-8692600	Weak transcription	Brain Angular Gyrus	brain
21	chr9:8692200-8693600	Weak transcription	Fetal Kidney	kidney
22	chr9:8692200-8696200	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr9:8692400-8693400	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr9:8692400-8697000	Enhancers	HUES64 Cell Line	embryonic stem cell

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