Variant report

Variant	rs10975643
Chromosome Location	chr9:6558502-6558503
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr9:6557666-6558888	H1-neurons	neurons:	n/a	n/a
2	POLR2A	chr9:6557659-6558740	H1-neurons	neurons:	n/a	n/a
3	EP300	chr9:6557734-6558562	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr9:6557726-6558763	H1-neurons	neurons:	n/a	n/a
5	REST	chr9:6557452-6559031	H1-neurons	neurons:	n/a	n/a

Variant related genes	Relation type
GLDC	TF binding region

Extended variants
information (count: 22 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:22 , 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
21	nsv892164	chr9:6555079-6664282	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
22	nsv931094	chr9:6558442-6672439	ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6510400-6558800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr9:6530800-6563200	Weak transcription	A549	lung
3	chr9:6532000-6570400	Strong transcription	Liver	Liver
4	chr9:6533200-6559800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr9:6547200-6560600	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr9:6553000-6560400	Weak transcription	Placenta	Placenta
7	chr9:6553400-6561600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr9:6553400-6563000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr9:6554400-6561800	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr9:6554600-6568600	Weak transcription	Fetal Intestine Small	intestine
11	chr9:6556000-6563200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr9:6556000-6566800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr9:6556800-6559400	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr9:6557000-6564600	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr9:6557200-6559200	Enhancers	Fetal Brain Male	brain
16	chr9:6557600-6559200	Strong transcription	H9 Cell Line	embryonic stem cell
17	chr9:6557600-6559200	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr9:6557800-6558600	Genic enhancers	H1 Cell Line	embryonic stem cell
19	chr9:6557800-6558600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr9:6557800-6558800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr9:6557800-6558800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr9:6557800-6558800	Flanking Active TSS	Brain Germinal Matrix	brain
23	chr9:6557800-6559200	Enhancers	Fetal Brain Female	brain
24	chr9:6557800-6562400	Strong transcription	HepG2	liver
25	chr9:6558000-6558600	Genic enhancers	HUES64 Cell Line	embryonic stem cell
26	chr9:6558000-6558600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr9:6558000-6558600	Active TSS	Brain Substantia Nigra	brain
28	chr9:6558000-6558800	Genic enhancers	HUES6 Cell Line	embryonic stem cell
29	chr9:6558000-6560200	Strong transcription	GM12878-XiMat	blood
30	chr9:6558200-6558600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr9:6558200-6558600	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
32	chr9:6558200-6558600	Enhancers	Brain Hippocampus Middle	brain
33	chr9:6558200-6558800	Genic enhancers	iPS-15b Cell Line	embryonic stem cell
34	chr9:6558200-6559000	Genic enhancers	iPS-18 Cell Line	embryonic stem cell
35	chr9:6558200-6559200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr9:6558400-6558600	Enhancers	Brain Anterior Caudate	brain
37	chr9:6558400-6558600	Enhancers	Brain Cingulate Gyrus	brain
38	chr9:6558400-6558800	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr9:6558400-6559000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr9:6558400-6559200	Enhancers	HUVEC	blood vessel
41	chr9:6558400-6563000	Weak transcription	NH-A	brain
42	chr9:6558400-6564600	Weak transcription	Brain Inferior Temporal Lobe	brain

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