Variant report

Variant	rs541070080
Chromosome Location	chr5:9543349-9543350
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	RAD21	chr5:9543246-9543876	IMR90	lung:	n/a	n/a
2	POLR2A	chr5:9542366-9543907	IMR90	lung:	n/a	n/a
3	RAD21	chr5:9543314-9545824	SK-N-SH	brain:	n/a	chr5:9545787-9545801 chr5:9544752-9544771 chr5:9544754-9544766 chr5:9545801-9545811 chr5:9544756-9544766 chr5:9545295-9545305

Variant related genes	Relation type
SNHG18	TF binding region

Extended variants
information (count: 26 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:26 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881438	chr5:8728874-9695667	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
2	nsv1015378	chr5:9053542-9617963	Genic enhancers Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
3	nsv537640	chr5:9053542-9617963	Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
4	nsv597071	chr5:9182376-9760599	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1032672	chr5:9182409-9843893	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv1035075	chr5:9182584-9843723	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv537641	chr5:9182584-9843723	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv1034637	chr5:9182784-9741743	Genic enhancers Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv537642	chr5:9182784-9741743	Enhancers Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	nsv1028656	chr5:9196001-9837040	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv1016885	chr5:9218932-9575594	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv1026078	chr5:9222811-9591290	Enhancers ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv1022137	chr5:9225121-9745434	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
14	nsv537643	chr5:9225121-9745434	Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
15	nsv1022574	chr5:9314645-9647238	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
16	nsv869120	chr5:9491731-10149255	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
17	nsv1018275	chr5:9504897-9560199	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
18	nsv537644	chr5:9504897-9560199	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
19	nsv597073	chr5:9533854-9550642	Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
20	esv1824536	chr5:9539540-9546237	Transcr. at gene 5' and 3' Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
21	esv1817081	chr5:9539540-9546451	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
22	nsv597074	chr5:9541866-9546412	Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
23	nsv597075	chr5:9542529-9546412	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
24	esv1803881	chr5:9542529-9546451	Bivalent/Poised TSS Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
25	nsv597076	chr5:9542529-9546451	Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
26	nsv1023329	chr5:9543307-9731720	Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:9521200-9544400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:9528400-9544200	Weak transcription	Fetal Intestine Small	intestine
3	chr5:9529600-9544400	Weak transcription	Pancreas	Pancrea
4	chr5:9529600-9544800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr5:9530200-9543600	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr5:9530200-9544600	Weak transcription	Lung	lung
7	chr5:9530400-9544200	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr5:9530400-9544800	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr5:9533400-9543600	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr5:9535800-9544000	Weak transcription	Fetal Stomach	stomach
11	chr5:9537400-9544200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr5:9538000-9544400	Weak transcription	Liver	Liver
13	chr5:9538600-9544400	Weak transcription	Left Ventricle	heart
14	chr5:9539400-9544400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr5:9541000-9544400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr5:9541800-9543800	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr5:9542600-9543800	Flanking Active TSS	Fetal Heart	heart
18	chr5:9542800-9543400	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr5:9542800-9543400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr5:9542800-9544200	Enhancers	Brain Substantia Nigra	brain
21	chr5:9542800-9547200	Active TSS	Breast Myoepithelial Primary Cells	Breast
22	chr5:9542800-9548400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr5:9543000-9543400	Flanking Active TSS	Placenta Amnion	Placenta Amnion
24	chr5:9543000-9543400	Flanking Active TSS	NHLF	lung
25	chr5:9543000-9543600	Enhancers	Fetal Lung	lung
26	chr5:9543000-9543800	Flanking Active TSS	Fetal Muscle Leg	muscle
27	chr5:9543000-9544000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr5:9543000-9544000	Enhancers	Muscle Satellite Cultured Cells	--
29	chr5:9543000-9544200	Flanking Active TSS	NHDF-Ad	bronchial
30	chr5:9543000-9544600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr5:9543000-9545000	Active TSS	Brain Germinal Matrix	brain
32	chr5:9543000-9545200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr5:9543000-9547200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr5:9543000-9547200	Active TSS	Brain Inferior Temporal Lobe	brain
35	chr5:9543000-9547800	Active TSS	Brain Hippocampus Middle	brain
36	chr5:9543000-9548200	Active TSS	Aorta	Aorta
37	chr5:9543200-9543400	Flanking Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr5:9543200-9543400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr5:9543200-9543400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr5:9543200-9543400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
41	chr5:9543200-9543400	Active TSS	Osteobl	bone
42	chr5:9543200-9543600	Active TSS	Brain Cingulate Gyrus	brain
43	chr5:9543200-9543600	Active TSS	Fetal Kidney	kidney
44	chr5:9543200-9543600	Enhancers	Ovary	ovary
45	chr5:9543200-9543800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr5:9543200-9544000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr5:9543200-9544000	Active TSS	Duodenum Mucosa	Duodenum
48	chr5:9543200-9544000	Flanking Active TSS	HMEC	breast
49	chr5:9543200-9544000	Flanking Active TSS	NH-A	brain
50	chr5:9543200-9544200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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