Variant report

Variant	rs7854679
Chromosome Location	chr9:6549370-6549371
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10465093	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10815441	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10975637	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12347488	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12685035	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13302691	0.82[AFR][1000 genomes]
rs16924678	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16924682	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1811943	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2282158	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2297443	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34267359	0.82[AFR][1000 genomes]
rs34948145	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3818705	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs55736048	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7858290	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031086	chr9:5806949-6630686	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv539967	chr9:5806949-6630686	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv933124	chr9:6099101-6644738	Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv1029000	chr9:6188652-6687205	Enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
5	nsv1031459	chr9:6216913-6657192	Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv948562	chr9:6222553-6684955	Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
7	nsv1032350	chr9:6328167-6630686	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv831497	chr9:6377501-6612402	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
9	nsv892162	chr9:6480005-6788085	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
10	nsv831498	chr9:6496021-6689728	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
11	nsv934176	chr9:6517535-6644738	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv892163	chr9:6523056-6632061	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv1025627	chr9:6523056-6648098	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
14	esv2752308	chr9:6523060-6899149	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
15	nsv613206	chr9:6525753-6686738	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
16	esv3324686	chr9:6528411-6728310	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
17	nsv1028402	chr9:6542253-6874231	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
18	nsv1018308	chr9:6544766-6869653	Genic enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
19	nsv1015462	chr9:6544766-6874231	Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
20	nsv1018870	chr9:6548393-6708345	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	49 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	chr9:6498800-6554400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr9:6510400-6558800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr9:6528600-6558000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr9:6530800-6563200	Weak transcription	A549	lung
5	chr9:6532000-6570400	Strong transcription	Liver	Liver
6	chr9:6533200-6559800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr9:6534600-6558200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr9:6535200-6549600	Weak transcription	Placenta	Placenta
9	chr9:6536000-6549400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr9:6536400-6549600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr9:6543600-6551200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr9:6543600-6551400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr9:6543600-6551800	Weak transcription	Brain Cingulate Gyrus	brain
14	chr9:6544000-6554600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr9:6544400-6558000	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr9:6545600-6551000	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr9:6545600-6554400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr9:6547000-6557800	Weak transcription	Brain Hippocampus Middle	brain
19	chr9:6547200-6560600	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr9:6547600-6551600	Strong transcription	GM12878-XiMat	blood
21	chr9:6548000-6558000	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr9:6548200-6549600	Enhancers	Fetal Brain Male	brain
23	chr9:6548200-6550200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr9:6548400-6550200	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr9:6548400-6550200	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr9:6548400-6551000	Strong transcription	H9 Cell Line	embryonic stem cell
27	chr9:6548400-6557800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr9:6548600-6549400	Enhancers	Fetal Brain Female	brain
29	chr9:6548600-6549600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr9:6548600-6549600	Enhancers	Fetal Muscle Trunk	muscle
31	chr9:6548600-6550200	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr9:6548600-6550400	Strong transcription	H1 Cell Line	embryonic stem cell
33	chr9:6548600-6551200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr9:6548800-6549400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
35	chr9:6549000-6549800	Flanking Active TSS	Brain Germinal Matrix	brain
36	chr9:6549000-6551600	Weak transcription	HSMM	muscle
37	chr9:6549000-6557800	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr9:6549200-6549400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr9:6549200-6549600	Enhancers	Fetal Muscle Leg	muscle
40	chr9:6549200-6550800	Weak transcription	HSMMtube	muscle
41	chr9:6549200-6551600	Strong transcription	HepG2	liver

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