Variant report

Variant	rs58377678
Chromosome Location	chr9:21813718-21813719
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	CTCF	chr9:21813640-21813790	GM12874	blood:	n/a	n/a
2	MAFK	chr9:21813671-21814247	HepG2	liver:	n/a	chr9:21813737-21813751 chr9:21813738-21813749 chr9:21813734-21813749 chr9:21813729-21813749 chr9:21813734-21813750 chr9:21813738-21813749
3	SMC3	chr9:21812785-21814442	SK-N-SH	brain:	n/a	chr9:21814038-21814052 chr9:21813156-21813170
4	CTCF	chr9:21813640-21813730	GM10248	blood:	n/a	n/a
5	CTCF	chr9:21813580-21813730	AoAF	blood vessel:	n/a	n/a
6	CTCF	chr9:21813580-21813730	GM12871	blood:	n/a	n/a
7	MAFK	chr9:21813670-21814234	Hela-S3	cervix:	n/a	chr9:21813737-21813751 chr9:21813738-21813749 chr9:21813734-21813749 chr9:21813729-21813749 chr9:21813734-21813750 chr9:21813738-21813749
8	CTCF	chr9:21812469-21814351	SK-N-SH	brain:	n/a	chr9:21814037-21814053 chr9:21813156-21813177 chr9:21813155-21813171 chr9:21814039-21814052 chr9:21813430-21813443 chr9:21813154-21813172 chr9:21813157-21813165 chr9:21814036-21814054 chr9:21814038-21814059 chr9:21814012-21814020
9	CTCF	chr9:21813660-21813810	AoAF	blood vessel:	n/a	n/a
10	RAD21	chr9:21812732-21814635	SK-N-SH	brain:	n/a	chr9:21813156-21813165 chr9:21813155-21813174 chr9:21813429-21813442 chr9:21814037-21814056 chr9:21814041-21814050 chr9:21813156-21813170 chr9:21813154-21813168 chr9:21813153-21813166
11	SMC3	chr9:21812326-21814372	Hela-S3	cervix:	n/a	chr9:21814038-21814052 chr9:21813156-21813170
12	CTCF	chr9:21813686-21813770	Spleen_OC	spleen:	n/a	n/a
13	POLR2A	chr9:21811561-21814235	Hela-S3	cervix:	n/a	n/a
14	CTCF	chr9:21813640-21813790	HEK293	kidney:	n/a	n/a
15	MAFF	chr9:21813610-21814212	HepG2	liver:	n/a	n/a
16	RAD21	chr9:21813716-21814458	HCT-116	colon:	n/a	chr9:21814037-21814056 chr9:21814041-21814050
17	CTCF	chr9:21813620-21813770	GM12872	blood:	n/a	n/a
18	CTCF	chr9:21812853-21814261	GM12878	blood:	n/a	chr9:21814037-21814053 chr9:21813156-21813177 chr9:21813155-21813171 chr9:21814039-21814052 chr9:21813430-21813443 chr9:21813154-21813172 chr9:21813157-21813165 chr9:21814036-21814054 chr9:21814038-21814059 chr9:21814012-21814020
19	TCF12	chr9:21812823-21814397	A549	lung:	n/a	chr9:21813189-21813199 chr9:21813499-21813506
20	RAD21	chr9:21813612-21814426	A549	lung:	n/a	chr9:21814037-21814056 chr9:21814041-21814050
21	CTCF	chr9:21813656-21814466	HCT-116	colon:	n/a	chr9:21814037-21814053 chr9:21814039-21814052 chr9:21814036-21814054 chr9:21814038-21814059 chr9:21814012-21814020
22	CTCF	chr9:21813620-21813770	SK-N-SH_RA	brain:	n/a	n/a
23	POLR2A	chr9:21812560-21814298	MCF-7	breast:	n/a	n/a
24	RUNX3	chr9:21813657-21814292	GM12878	blood:	n/a	n/a
25	CTCF	chr9:21812791-21814543	A549	lung:	n/a	chr9:21814037-21814053 chr9:21813156-21813177 chr9:21813155-21813171 chr9:21814039-21814052 chr9:21813430-21813443 chr9:21813154-21813172 chr9:21813157-21813165 chr9:21814036-21814054 chr9:21814038-21814059 chr9:21814012-21814020
26	RFX5	chr9:21812760-21814441	IMR90	lung:	n/a	chr9:21813740-21813748
27	EBF1	chr9:21813573-21814103	GM12878	blood:	n/a	chr9:21813705-21813718 chr9:21813705-21813716 chr9:21813707-21813716 chr9:21813758-21813769 chr9:21813707-21813716
28	MAFK	chr9:21813574-21814157	HepG2	liver:	n/a	chr9:21813737-21813751 chr9:21813738-21813749 chr9:21813734-21813749 chr9:21813729-21813749 chr9:21813734-21813750 chr9:21813738-21813749
29	RAD21	chr9:21813708-21814398	IMR90	lung:	n/a	chr9:21814037-21814056 chr9:21814041-21814050
30	CTCF	chr9:21813600-21813750	GM12864	blood:	n/a	n/a
31	POLR2A	chr9:21812880-21814247	HCT-116	colon:	n/a	n/a
32	WRNIP1	chr9:21812951-21814142	GM12878	blood:	n/a	n/a
33	CTCF	chr9:21813660-21813810	GM12870	blood:	n/a	n/a
34	RAD21	chr9:21812802-21814311	HCT-116	colon:	n/a	chr9:21813156-21813165 chr9:21813155-21813174 chr9:21813429-21813442 chr9:21814037-21814056 chr9:21814041-21814050 chr9:21813156-21813170 chr9:21813154-21813168 chr9:21813153-21813166
35	POLR2A	chr9:21811752-21814285	A549	lung:	n/a	n/a
36	SMC3	chr9:21812983-21814373	GM12878	blood:	n/a	chr9:21814038-21814052 chr9:21813156-21813170
37	TCF7L2	chr9:21813632-21814354	HEK293	kidney:	n/a	chr9:21814054-21814064 chr9:21814055-21814064 chr9:21814053-21814067

No.	Distal block	Cell Line	Cell type
1	chr9:21813108..21815129-chr9:22001503..22004148,2	MCF-7	breast:
2	chr9:21812476..21814067-chr9:22243888..22245328,7	MCF-7	breast:
3	chr9:21811237..21820561-chr9:21988636..21997115,18	MCF-7	breast:
4	chr9:21811532..21820564-chr9:21988281..21997291,17	MCF-7	breast:
5	chr9:21812786..21814111-chr9:22238617..22239873,5	MCF-7	breast:
6	chr9:21813615..21814422-chr9:22119086..22119968,3	MCF-7	breast:
7	chr9:21813352..21815256-chr9:22105449..22107592,2	MCF-7	breast:
8	chr9:21813642..21814532-chr9:22008558..22009208,2	MCF-7	breast:

Variant related genes	Relation type
TUBB8P1	TF binding region
ENSG00000147889	Chromatin interaction
ENSG00000266446	Chromatin interaction
ENSG00000147883	Chromatin interaction
ENSG00000240498	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10114559	0.91[ASN][1000 genomes]
rs10119568	0.85[ASN][1000 genomes]
rs10119693	0.84[ASN][1000 genomes]
rs10121449	0.90[ASN][1000 genomes]
rs10738601	0.84[ASN][1000 genomes]
rs10757257	0.88[ASN][1000 genomes]
rs10811623	0.88[ASN][1000 genomes]
rs10811625	0.90[ASN][1000 genomes]
rs10811626	0.90[ASN][1000 genomes]
rs10811629	0.84[ASN][1000 genomes]
rs10965128	0.82[ASN][1000 genomes]
rs10965134	0.82[ASN][1000 genomes]
rs10965135	0.82[ASN][1000 genomes]
rs10965141	0.88[ASN][1000 genomes]
rs10965143	0.90[ASN][1000 genomes]
rs10965144	0.90[ASN][1000 genomes]
rs10965145	0.90[ASN][1000 genomes]
rs10965153	0.82[ASN][1000 genomes]
rs11523031	0.84[ASN][1000 genomes]
rs1345020	0.81[ASN][1000 genomes]
rs1345023	0.80[ASN][1000 genomes]
rs1345024	0.80[ASN][1000 genomes]
rs3900787	0.90[ASN][1000 genomes]
rs3922992	0.90[ASN][1000 genomes]
rs4615669	0.90[ASN][1000 genomes]
rs4977567	0.83[ASN][1000 genomes]
rs4977733	0.84[ASN][1000 genomes]
rs7022754	0.82[ASN][1000 genomes]
rs7023329	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7023954	0.91[ASN][1000 genomes]
rs7049092	0.82[ASN][1000 genomes]
rs7863090	0.90[ASN][1000 genomes]
rs7863942	0.81[ASN][1000 genomes]
rs7868783	0.84[ASN][1000 genomes]
rs958219	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529609	chr9:21708371-22537069	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv8426	chr9:21763810-22176200	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21804000-21814200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr9:21804000-21817600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:21804000-21838200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr9:21804400-21816000	Weak transcription	Fetal Kidney	kidney
5	chr9:21805000-21816200	Weak transcription	Fetal Brain Male	brain
6	chr9:21806000-21817600	Genic enhancers	HMEC	breast
7	chr9:21806400-21819800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr9:21806600-21815800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr9:21806600-21841200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr9:21806800-21815800	Weak transcription	Brain Germinal Matrix	brain
11	chr9:21809200-21836800	Weak transcription	Small Intestine	intestine
12	chr9:21809800-21813800	Genic enhancers	NHEK	skin
13	chr9:21809800-21814400	Genic enhancers	A549	lung
14	chr9:21810800-21813800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr9:21811000-21815600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr9:21811600-21813800	Enhancers	Placenta	Placenta
17	chr9:21811600-21814000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr9:21811600-21815600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr9:21811600-21815800	Weak transcription	Fetal Brain Female	brain
20	chr9:21811800-21813800	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr9:21812000-21813800	Enhancers	HUVEC	blood vessel
22	chr9:21812000-21814200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr9:21812000-21814400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr9:21812000-21814400	Enhancers	Hela-S3	cervix
25	chr9:21812000-21815600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr9:21812000-21815600	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr9:21812200-21814400	Enhancers	Muscle Satellite Cultured Cells	--
28	chr9:21812200-21814800	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr9:21812200-21815600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr9:21812200-21815600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr9:21812200-21815600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr9:21812200-21815600	Weak transcription	Aorta	Aorta
33	chr9:21812200-21815600	Weak transcription	Fetal Muscle Leg	muscle
34	chr9:21812200-21815600	Weak transcription	Gastric	stomach
35	chr9:21812200-21815600	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr9:21812200-21815800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr9:21812200-21815800	Weak transcription	Thymus	Thymus
38	chr9:21812200-21816000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr9:21812200-21817000	Weak transcription	Fetal Intestine Small	intestine
40	chr9:21812200-21817200	Weak transcription	Esophagus	oesophagus
41	chr9:21812200-21817400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr9:21812400-21813800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr9:21812400-21813800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
44	chr9:21812400-21814000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr9:21812400-21814400	Enhancers	NH-A	brain
46	chr9:21812400-21814600	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr9:21812400-21814600	Enhancers	Skeletal Muscle Male	skeletal muscle
48	chr9:21812400-21815400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr9:21812400-21815600	Weak transcription	Fetal Lung	lung
50	chr9:21812600-21813800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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