Variant report

Variant	rs10118880
Chromosome Location	chr9:21559961-21559962
allele	A/G
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	MAX	chr9:21558675-21560428	Hela-S3	cervix:	n/a	n/a
2	MAZ	chr9:21559103-21560489	Hela-S3	cervix:	n/a	n/a
3	BCL3	chr9:21558143-21560436	A549	lung:	n/a	chr9:21559960-21559973
4	MAFK	chr9:21559767-21560832	Hela-S3	cervix:	n/a	chr9:21560184-21560200
5	POLR2A	chr9:21559143-21560567	A549	lung:	n/a	n/a
6	JUND	chr9:21559847-21560198	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr9:21558363-21560420	IMR90	lung:	n/a	n/a
8	ATF3	chr9:21558990-21560411	A549	lung:	n/a	chr9:21559784-21559793
9	SIN3AK20	chr9:21559084-21560169	PANC-1	pancreas:	n/a	n/a
10	RCOR1	chr9:21559180-21560213	Hela-S3	cervix:	n/a	n/a
11	SP1	chr9:21558826-21560965	A549	lung:	n/a	chr9:21560873-21560887
12	POLR2A	chr9:21559096-21560187	A549	lung:	n/a	n/a
13	POLR2A	chr9:21559633-21560139	SK-N-MC	brain:	n/a	n/a
14	POLR2A	chr9:21559514-21560196	HEK293	kidney:	n/a	n/a
15	RAD21	chr9:21559566-21560258	A549	lung:	n/a	n/a
16	MAX	chr9:21558964-21559971	H1-hESC	embryonic stem cell:	n/a	n/a
17	JUND	chr9:21559387-21559975	A549	lung:	n/a	n/a
18	POLR2A	chr9:21558519-21560214	Hela-S3	cervix:	n/a	n/a
19	TAF1	chr9:21558798-21560217	A549	lung:	n/a	n/a
20	GABPA	chr9:21559861-21560532	A549	lung:	n/a	n/a
21	POLR2A	chr9:21558211-21560315	HUVEC	blood vessel:	n/a	n/a
22	GATA3	chr9:21558277-21560408	A549	lung:	n/a	n/a
23	POLR2A	chr9:21558505-21560994	PANC-1	pancreas:	n/a	n/a
24	POLR2A	chr9:21559426-21560289	HUVEC	blood vessel:	n/a	n/a
25	POLR2A	chr9:21559080-21560234	A549	lung:	n/a	n/a
26	SMC3	chr9:21558701-21560142	Hela-S3	cervix:	n/a	n/a
27	CREB1	chr9:21559201-21560113	A549	lung:	n/a	n/a
28	POLR2A	chr9:21559627-21560173	ECC-1	luminal epithelium:	n/a	n/a
29	ZKSCAN1	chr9:21559261-21559966	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr9:21557847-21560219	MCF10A-Er-Src	breast:	n/a	n/a
31	MAZ	chr9:21558898-21560510	IMR90	lung:	n/a	n/a
32	RAD21	chr9:21559541-21560062	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr9:21558457-21560655	Hela-S3	cervix:	n/a	n/a
34	JUND	chr9:21559025-21560321	A549	lung:	n/a	n/a
35	POLR2A	chr9:21558574-21560434	Hela-S3	cervix:	n/a	n/a
36	E2F6	chr9:21558957-21560541	H1-hESC	embryonic stem cell:	n/a	chr9:21559333-21559344 chr9:21559333-21559344 chr9:21559328-21559343 chr9:21559676-21559686 chr9:21559333-21559344
37	POLR2A	chr9:21558140-21560925	PANC-1	pancreas:	n/a	n/a
38	POLR2A	chr9:21559120-21560170	A549	lung:	n/a	n/a
39	TCF7L2	chr9:21559317-21560213	HCT-116	colon:	n/a	n/a
40	EGR1	chr9:21559660-21560105	H1-hESC	embryonic stem cell:	n/a	chr9:21559828-21559842 chr9:21559881-21559895
41	POLR2A	chr9:21558305-21560219	MCF10A-Er-Src	breast:	n/a	n/a
42	CHD2	chr9:21559411-21560568	Hela-S3	cervix:	n/a	n/a
43	POLR2A	chr9:21559588-21560127	H1-hESC	embryonic stem cell:	n/a	n/a
44	TBP	chr9:21559565-21560134	H1-hESC	embryonic stem cell:	n/a	n/a
45	MAX	chr9:21558891-21560590	A549	lung:	n/a	n/a
46	POLR2A	chr9:21558630-21560738	Hela-S3	cervix:	n/a	n/a
47	BCL3	chr9:21558965-21560497	A549	lung:	n/a	chr9:21559960-21559973
48	TCF12	chr9:21559500-21560147	A549	lung:	n/a	chr9:21559806-21559813
49	POLR2A	chr9:21559558-21560785	HCT-116	colon:	n/a	n/a
50	CEBPB	chr9:21559583-21560780	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:74230065..74230819-chr9:21559626..21560366,2	Hela-S3	cervix:
2	chr1:149223886..149224467-chr9:21559638..21560548,2	Hela-S3	cervix:
3	chr7:100026744..100027492-chr9:21559602..21560168,2	Hela-S3	cervix:

Variant related genes	Relation type
MIR31HG	TF binding region
ENSG00000146834	Chromatin interaction
ENSG00000156508	Chromatin interaction
ENSG00000206737	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10126000	0.82[ASN][1000 genomes]
rs1013241	0.88[ASN][1000 genomes]
rs10738594	0.89[EUR][1000 genomes]
rs10757225	0.89[EUR][1000 genomes]
rs10965064	0.88[EUR][1000 genomes]
rs1545749	0.80[EUR][1000 genomes]
rs1983811	0.81[EUR][1000 genomes]
rs4141712	0.89[EUR][1000 genomes]
rs4141713	0.92[EUR][1000 genomes]
rs7033598	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7872217	0.86[ASN][1000 genomes]
rs9298816	0.92[EUR][1000 genomes]
rs9298817	0.82[EUR][1000 genomes]
rs9657572	0.86[EUR][1000 genomes]
rs9657607	0.88[EUR][1000 genomes]
rs996442	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031432	chr9:21472601-21608774	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	122 gene(s)	inside rSNPs	diseases
2	nsv540085	chr9:21472601-21608774	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	122 gene(s)	inside rSNPs	diseases
3	nsv1029634	chr9:21542970-21765286	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	esv3406465	chr9:21558577-21561125	Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21554800-21560600	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr9:21555200-21560000	Active TSS	Hela-S3	cervix
3	chr9:21555200-21560800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr9:21555800-21560200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr9:21556200-21560000	Active TSS	HMEC	breast
6	chr9:21556200-21560200	Active TSS	NH-A	brain
7	chr9:21556200-21560200	Active TSS	Osteobl	bone
8	chr9:21556200-21560400	Active TSS	NHLF	lung
9	chr9:21556400-21560000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr9:21556400-21560400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr9:21556400-21560600	Active TSS	NHDF-Ad	bronchial
12	chr9:21556600-21560200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr9:21557000-21560400	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
14	chr9:21557400-21560000	Active TSS	HUVEC	blood vessel
15	chr9:21558200-21560200	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr9:21558200-21560200	Bivalent/Poised TSS	Fetal Intestine Large	intestine
17	chr9:21558200-21560400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
18	chr9:21558200-21560600	Active TSS	HSMM	muscle
19	chr9:21558200-21560800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
20	chr9:21558400-21560200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr9:21558400-21560400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr9:21558400-21560400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
23	chr9:21558600-21560000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr9:21558600-21560000	Bivalent/Poised TSS	Fetal Intestine Small	intestine
25	chr9:21558600-21560000	Bivalent/Poised TSS	Fetal Stomach	stomach
26	chr9:21558600-21560200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr9:21558600-21560200	Active TSS	H9 Cell Line	embryonic stem cell
28	chr9:21558600-21560200	Active TSS	Gastric	stomach
29	chr9:21558600-21560400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
30	chr9:21558600-21560400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr9:21558600-21560400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr9:21558600-21560400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
33	chr9:21558600-21560400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr9:21558600-21560400	Bivalent/Poised TSS	Esophagus	oesophagus
35	chr9:21558600-21560600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
36	chr9:21558600-21560600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr9:21558600-21560600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr9:21558600-21560600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr9:21558600-21560600	Active TSS	HSMMtube	muscle
40	chr9:21558800-21560000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr9:21558800-21560000	Bivalent/Poised TSS	GM12878-XiMat	blood
42	chr9:21558800-21560200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
43	chr9:21558800-21560200	Bivalent/Poised TSS	Stomach Mucosa	stomach
44	chr9:21558800-21560400	Active TSS	Primary T killer memory cells from peripheral blood	blood
45	chr9:21558800-21560400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr9:21558800-21560400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
47	chr9:21558800-21560600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
48	chr9:21558800-21560600	Active TSS	Placenta Amnion	Placenta Amnion
49	chr9:21559000-21560000	Active TSS	Right Atrium	heart
50	chr9:21559000-21560200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell

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