Variant report

Variant	rs4840393
Chromosome Location	chr8:8962666-8962667
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11776300	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11782937	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13248595	0.95[EUR][1000 genomes]
rs13256068	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13264785	1.00[CEU][hapmap];0.96[GIH][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes]
rs1445494	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1445495	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17155242	0.82[ASN][1000 genomes]
rs1809006	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2898208	0.98[ASN][1000 genomes]
rs4840392	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4841098	0.90[EUR][1000 genomes]
rs4841099	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4841100	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4841101	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4841102	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56106119	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6601289	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7014850	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7465439	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9650629	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv890331	chr8:8093240-8971100	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv917117	chr8:8621658-9313799	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv1022468	chr8:8857853-9209167	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv539460	chr8:8857853-9209167	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv817373	chr8:8857854-9361049	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
6	nsv523098	chr8:8944307-8982396	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv526092	chr8:8944307-8982396	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1022328	chr8:8954003-9061281	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
9	esv2761405	chr8:8960271-8967105	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
10	nsv610206	chr8:8961017-9162048	Genic enhancers Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4840393	FLJ10661	cis	lymphoblastoid	seeQTL
rs4840393	MFHAS1	cis	cerebellum	SCAN
rs4840393	CTSB	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:8956800-8968000	Enhancers	Fetal Intestine Large	intestine
2	chr8:8957200-8963800	Enhancers	Fetal Intestine Small	intestine
3	chr8:8958200-8963800	Enhancers	Stomach Mucosa	stomach
4	chr8:8959000-8963400	Enhancers	Liver	Liver
5	chr8:8959600-8963400	Enhancers	Placenta Amnion	Placenta Amnion
6	chr8:8960400-8966600	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr8:8960600-8966800	Weak transcription	Right Atrium	heart
8	chr8:8960800-8962800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr8:8960800-8963200	Enhancers	Rectal Mucosa Donor 31	rectum
10	chr8:8960800-8967800	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr8:8961000-8963600	Enhancers	Duodenum Mucosa	Duodenum
12	chr8:8961000-8966400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr8:8961200-8965600	Weak transcription	K562	blood
14	chr8:8961200-8966400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr8:8961200-8966400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr8:8961400-8963000	Enhancers	Sigmoid Colon	Sigmoid Colon
17	chr8:8961400-8966600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr8:8961600-8963200	Weak transcription	A549	lung
19	chr8:8961600-8963600	Enhancers	Placenta	Placenta
20	chr8:8961600-8963800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr8:8961600-8966400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr8:8961800-8962800	Enhancers	Fetal Lung	lung
23	chr8:8961800-8968000	Enhancers	Fetal Heart	heart
24	chr8:8962000-8965800	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr8:8962000-8991400	Weak transcription	Psoas Muscle	Psoas
26	chr8:8962200-8966600	Weak transcription	Left Ventricle	heart
27	chr8:8962200-8967400	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr8:8962600-8965800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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