Variant report

Variant	rs563556701
Chromosome Location	chr9:2620975-2620976
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	POLR2A	chr9:2620945-2622528	U87	brain:	n/a	n/a
2	REST	chr9:2620800-2623973	H1-neurons	neurons:	n/a	chr9:2621948-2621961 chr9:2622878-2622891 chr9:2621769-2621787 chr9:2621771-2621784 chr9:2622822-2622842
3	TBP	chr9:2620958-2621701	H1-hESC	embryonic stem cell:	n/a	n/a
4	CHD1	chr9:2620886-2622127	IMR90	lung:	n/a	n/a
5	MAX	chr9:2620942-2624127	A549	lung:	n/a	chr9:2623485-2623494 chr9:2623484-2623495 chr9:2623484-2623495 chr9:2623668-2623678
6	MAZ	chr9:2620701-2624354	IMR90	lung:	n/a	chr9:2623485-2623494 chr9:2623484-2623495 chr9:2623484-2623495
7	RCOR1	chr9:2620557-2622180	IMR90	lung:	n/a	n/a
8	POLR2A	chr9:2620818-2621959	H1-hESC	embryonic stem cell:	n/a	n/a
9	MXI1	chr9:2619904-2624722	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr9:2620935-2623409	H1-neurons	neurons:	n/a	n/a
11	SIN3A	chr9:2620917-2624227	H1-hESC	embryonic stem cell:	n/a	chr9:2621427-2621438 chr9:2623544-2623553 chr9:2621915-2621924
12	POLR2A	chr9:2620945-2622204	U87	brain:	n/a	n/a
13	TAF1	chr9:2620916-2622493	H1-neurons	neurons:	n/a	n/a
14	POLR2A	chr9:2620851-2623684	H1-neurons	neurons:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KIAA0020-1	chr9:2619998-2621792	NONHSAT130002

Variant related genes	Relation type
VLDLR	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1020530	chr9:1870197-2658587	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv530929	chr9:1998911-2925112	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv466078	chr9:2218129-2621030	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv613126	chr9:2218129-2621030	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv529508	chr9:2267812-2684272	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv916750	chr9:2430846-2826706	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	nsv531564	chr9:2452325-2700375	Flanking Bivalent TSS/Enh Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
8	nsv1017581	chr9:2494815-3172020	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
9	nsv539934	chr9:2494815-3172020	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
10	nsv1029876	chr9:2526760-2633562	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv892069	chr9:2600836-2631738	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv892070	chr9:2610307-2633921	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv518550	chr9:2618969-2621030	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv892071	chr9:2618969-2626031	Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
15	nsv892072	chr9:2619915-2623253	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
16	nsv824819	chr9:2620547-2623694	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
17	nsv892073	chr9:2620592-2627365	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:2614200-2621000	Weak transcription	Pancreas	Pancrea
2	chr9:2614200-2621200	Weak transcription	Lung	lung
3	chr9:2614400-2621000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr9:2616800-2621000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr9:2619800-2624000	Active TSS	Ovary	ovary
6	chr9:2620000-2624000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
7	chr9:2620000-2624200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr9:2620200-2621000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
9	chr9:2620200-2621000	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
10	chr9:2620200-2621000	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
11	chr9:2620200-2621000	Enhancers	Brain Substantia Nigra	brain
12	chr9:2620200-2621000	Active TSS	Stomach Smooth Muscle	stomach
13	chr9:2620200-2621400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr9:2620200-2621400	Bivalent/Poised TSS	Primary T cells from cord blood	blood
15	chr9:2620200-2623600	Active TSS	Brain Anterior Caudate	brain
16	chr9:2620400-2621400	Flanking Active TSS	Dnd41	blood
17	chr9:2620400-2622200	Active TSS	Fetal Brain Female	brain
18	chr9:2620400-2623200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
19	chr9:2620400-2623800	Active TSS	H9 Cell Line	embryonic stem cell
20	chr9:2620600-2621000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr9:2620600-2621000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr9:2620600-2621000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr9:2620600-2621000	Enhancers	Fetal Lung	lung
24	chr9:2620600-2621000	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr9:2620600-2621000	Bivalent Enhancer	HepG2	liver
26	chr9:2620600-2621200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr9:2620600-2621200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr9:2620600-2621200	Flanking Bivalent TSS/Enh	NHEK	skin
29	chr9:2620600-2621400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr9:2620600-2621400	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
31	chr9:2620600-2621400	Flanking Active TSS	Brain Germinal Matrix	brain
32	chr9:2620600-2621400	Flanking Active TSS	Fetal Brain Male	brain
33	chr9:2620600-2621600	Flanking Active TSS	Brain Hippocampus Middle	brain
34	chr9:2620600-2622400	Active TSS	Duodenum Smooth Muscle	Duodenum
35	chr9:2620600-2624000	Active TSS	Right Atrium	heart
36	chr9:2620600-2624200	Active TSS	Pancreatic Islets	Pancreatic Islet
37	chr9:2620800-2621000	Flanking Active TSS	H1 Cell Line	embryonic stem cell
38	chr9:2620800-2621000	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
39	chr9:2620800-2621000	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
40	chr9:2620800-2621000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr9:2620800-2621000	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
42	chr9:2620800-2621000	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
43	chr9:2620800-2621000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
44	chr9:2620800-2621000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr9:2620800-2621000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr9:2620800-2621000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
47	chr9:2620800-2621000	Flanking Active TSS	Fetal Heart	heart
48	chr9:2620800-2621000	Flanking Active TSS	Fetal Stomach	stomach
49	chr9:2620800-2621000	Enhancers	GM12878-XiMat	blood
50	chr9:2620800-2621000	Enhancers	HMEC	breast

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