Variant report

Variant	rs10780618
Chromosome Location	chr9:86236132-86236133
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	SMC3	chr9:86235630-86236516	HepG2	liver:	n/a	chr9:86235864-86235872 chr9:86235864-86235878
2	RAD21	chr9:86235629-86236143	MCF-7	breast:	n/a	chr9:86235868-86235880 chr9:86235863-86235882 chr9:86235862-86235876
3	TCF7L2	chr9:86235599-86236133	Hela-S3	cervix:	n/a	chr9:86235926-86235936 chr9:86235923-86235937 chr9:86235926-86235935 chr9:86235926-86235933
4	POLR2A	chr9:86235644-86236486	HepG2	liver:	n/a	n/a
5	HEY1	chr9:86236055-86236590	HepG2	liver:	n/a	n/a
6	RAD21	chr9:86235656-86236256	A549	lung:	n/a	chr9:86235868-86235880 chr9:86235863-86235882 chr9:86235862-86235876
7	EBF1	chr9:86235857-86236135	GM12878	blood:	n/a	n/a
8	RAD21	chr9:86235546-86236165	ECC-1	luminal epithelium:	n/a	chr9:86235868-86235880 chr9:86235863-86235882 chr9:86235862-86235876
9	RAD21	chr9:86235523-86236225	HCT-116	colon:	n/a	chr9:86235868-86235880 chr9:86235863-86235882 chr9:86235862-86235876
10	RAD21	chr9:86235616-86236197	HepG2	liver:	n/a	chr9:86235868-86235880 chr9:86235863-86235882 chr9:86235862-86235876
11	RAD21	chr9:86235493-86236271	HCT-116	colon:	n/a	chr9:86235868-86235880 chr9:86235863-86235882 chr9:86235862-86235876
12	TCF7L2	chr9:86235596-86236309	MCF-7	breast:	n/a	chr9:86235926-86235936 chr9:86235923-86235937 chr9:86235926-86235935 chr9:86235926-86235933
13	SMC3	chr9:86235666-86236136	GM12878	blood:	n/a	chr9:86235864-86235872 chr9:86235864-86235878
14	NFIC	chr9:86235683-86236146	HepG2	liver:	n/a	n/a
15	RAD21	chr9:86235614-86236148	ECC-1	luminal epithelium:	n/a	chr9:86235868-86235880 chr9:86235863-86235882 chr9:86235862-86235876
16	CTCF	chr9:86235602-86236175	MCF-7	breast:	n/a	chr9:86235863-86235879 chr9:86235864-86235885 chr9:86235865-86235878 chr9:86235865-86235873 chr9:86235862-86235880
17	MAX	chr9:86235624-86236172	NB4	blood:	n/a	n/a
18	HNF4A	chr9:86236132-86236553	HepG2	liver:	n/a	chr9:86236372-86236387
19	RFX5	chr9:86235650-86236181	HepG2	liver:	n/a	chr9:86235825-86235840
20	TEAD4	chr9:86235642-86236133	HepG2	liver:	n/a	n/a
21	MAFF	chr9:86235757-86236392	HepG2	liver:	n/a	n/a
22	TCF7L2	chr9:86235260-86236445	HepG2	liver:	n/a	chr9:86235926-86235936 chr9:86235923-86235937 chr9:86235926-86235935 chr9:86235926-86235933
23	RAD21	chr9:86235601-86236216	MCF-7	breast:	n/a	chr9:86235868-86235880 chr9:86235863-86235882 chr9:86235862-86235876
24	RCOR1	chr9:86235672-86236403	HepG2	liver:	n/a	n/a
25	CTCF	chr9:86236080-86236230	AG04450	lung:	n/a	n/a
26	CTCF	chr9:86234965-86236517	SK-N-SH	brain:	n/a	chr9:86235863-86235879 chr9:86235864-86235885 chr9:86235865-86235878 chr9:86235865-86235873 chr9:86235862-86235880
27	RAD21	chr9:86235662-86236403	HepG2	liver:	n/a	chr9:86235868-86235880 chr9:86235863-86235882 chr9:86235862-86235876
28	RAD21	chr9:86235599-86236184	A549	lung:	n/a	chr9:86235868-86235880 chr9:86235863-86235882 chr9:86235862-86235876
29	MAX	chr9:86235874-86236212	HepG2	liver:	n/a	n/a
30	CTCF	chr9:86235616-86236163	HCT-116	colon:	n/a	chr9:86235863-86235879 chr9:86235864-86235885 chr9:86235865-86235878 chr9:86235865-86235873 chr9:86235862-86235880
31	POLR2A	chr9:86236126-86236537	HepG2	liver:	n/a	n/a
32	CTCF	chr9:86234900-86236290	A549	lung:	n/a	chr9:86235863-86235879 chr9:86235864-86235885 chr9:86235865-86235878 chr9:86235865-86235873 chr9:86235862-86235880
33	FOXA1	chr9:86235971-86236480	HepG2	liver:	n/a	n/a
34	BHLHE40	chr9:86235749-86236425	HepG2	liver:	n/a	n/a
35	MYBL2	chr9:86235715-86236623	HepG2	liver:	n/a	n/a
36	FOXA1	chr9:86235910-86236628	HepG2	liver:	n/a	n/a
37	TBP	chr9:86235810-86236526	HepG2	liver:	n/a	n/a
38	CTBP2	chr9:86235720-86236219	H1-hESC	embryonic stem cell:	n/a	n/a
39	HEY1	chr9:86236118-86236589	HepG2	liver:	n/a	n/a
40	FOXA1	chr9:86235906-86236567	HepG2	liver:	n/a	n/a
41	TCF7L2	chr9:86235521-86236293	PANC-1	pancreas:	n/a	chr9:86235926-86235936 chr9:86235923-86235937 chr9:86235926-86235935 chr9:86235926-86235933
42	TCF7L2	chr9:86235644-86236263	HCT-116	colon:	n/a	chr9:86235926-86235936 chr9:86235923-86235937 chr9:86235926-86235935 chr9:86235926-86235933
43	SMC3	chr9:86235480-86236285	SK-N-SH	brain:	n/a	chr9:86235864-86235872 chr9:86235864-86235878
44	POLR2A	chr9:86235860-86236526	HepG2	liver:	n/a	n/a
45	TCF7L2	chr9:86235449-86236558	HEK293	kidney:	n/a	chr9:86235926-86235936 chr9:86235923-86235937 chr9:86235926-86235935 chr9:86235926-86235933
46	ZEB1	chr9:86235644-86236807	HepG2	liver:	n/a	n/a
47	POLR2A	chr9:86236115-86236606	HepG2	liver:	n/a	n/a
48	SP1	chr9:86235684-86236625	HepG2	liver:	n/a	n/a
49	CTCF	chr9:86235637-86236155	H1-hESC	embryonic stem cell:	n/a	chr9:86235863-86235879 chr9:86235864-86235885 chr9:86235865-86235878 chr9:86235865-86235873 chr9:86235862-86235880
50	MXI1	chr9:86235703-86236145	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:86235893..86237501-chr9:86238448..86240518,2	MCF-7	breast:
2	chr9:86235380..86236670-chr9:86263664..86264678,5	K562	blood:
3	chr9:86235380..86236346-chr9:86263721..86264658,5	MCF-7	breast:
4	chr9:86235404..86236308-chr9:86263503..86264783,10	MCF-7	breast:
5	chr9:86231903..86234223-chr9:86234502..86236689,2	MCF-7	breast:
6	chr9:86234634..86237562-chr9:86262513..86264120,2	MCF-7	breast:

Variant related genes	Relation type
IDNK	TF binding region

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10512136	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10512137	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes]
rs1056073	0.84[AMR][1000 genomes]
rs10746717	0.86[AMR][1000 genomes]
rs10780616	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10780617	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10780619	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10780620	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10780622	0.86[AMR][1000 genomes]
rs10780623	0.84[AMR][1000 genomes]
rs10780624	0.84[AMR][1000 genomes]
rs10780625	1.00[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap];0.86[AMR][1000 genomes]
rs10868035	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10868036	0.89[AMR][1000 genomes]
rs10868037	0.87[AMR][1000 genomes]
rs10868038	0.87[AMR][1000 genomes]
rs10868042	0.87[AMR][1000 genomes]
rs10868043	0.82[AMR][1000 genomes]
rs11140198	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[AMR][1000 genomes]
rs11140202	0.86[AMR][1000 genomes]
rs11140209	0.95[CEU][hapmap];0.86[AMR][1000 genomes]
rs11140212	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes]
rs11140221	0.86[AMR][1000 genomes]
rs11140223	0.80[AMR][1000 genomes]
rs11791175	0.86[CHB][hapmap];0.85[JPT][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1333861	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.81[YRI][hapmap];0.86[AMR][1000 genomes]
rs1333862	1.00[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes]
rs1537502	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1537503	0.95[CEU][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1961941	1.00[CEU][hapmap];0.81[CHB][hapmap];0.87[JPT][hapmap];0.84[AMR][1000 genomes]
rs2282220	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3750409	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3750410	0.95[CEU][hapmap];0.81[CHB][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3814505	1.00[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes]
rs4146740	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4454364	0.95[CEU][hapmap];0.86[AMR][1000 genomes]
rs4877790	0.90[AMR][1000 genomes]
rs4877791	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes]
rs4877793	0.86[AMR][1000 genomes]
rs4877794	1.00[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.87[AMR][1000 genomes]
rs4877796	0.95[CEU][hapmap];0.86[AMR][1000 genomes]
rs4877797	1.00[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.85[AMR][1000 genomes]
rs4877799	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes]
rs4877800	0.83[AMR][1000 genomes]
rs7046388	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72618136	0.86[AMR][1000 genomes]
rs7860614	0.86[AMR][1000 genomes]
rs7863266	0.86[AMR][1000 genomes]
rs7866234	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes]
rs7871055	0.90[CEU][hapmap];0.81[CHB][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs868917	1.00[CEU][hapmap];0.86[AMR][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	nsv893512	chr9:86022215-86323309	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv516587	chr9:86226119-86255765	Flanking Active TSS Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10780618	RP11-522I20.3	cis	Muscle Skeletal	GTEx
rs10780618	RP11-522I20.3	cis	Whole Blood	GTEx

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86216200-86237400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr9:86235400-86236200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr9:86235600-86236200	Enhancers	H1 Cell Line	embryonic stem cell
4	chr9:86235600-86236200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr9:86235600-86236200	Enhancers	Fetal Heart	heart
6	chr9:86235600-86236200	Active TSS	Rectal Smooth Muscle	rectum
7	chr9:86235600-86236200	Enhancers	GM12878-XiMat	blood
8	chr9:86235600-86236400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr9:86235600-86237400	Enhancers	Fetal Intestine Large	intestine
10	chr9:86235600-86237400	Enhancers	Fetal Intestine Small	intestine
11	chr9:86235600-86237400	Enhancers	Fetal Thymus	thymus
12	chr9:86235800-86236200	Active TSS	HUES48 Cell Line	embryonic stem cell
13	chr9:86235800-86236200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
14	chr9:86235800-86236200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr9:86235800-86236200	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr9:86235800-86236200	Enhancers	Primary neutrophils fromperipheralblood	blood
17	chr9:86235800-86236200	Enhancers	Primary B cells from peripheral blood	blood
18	chr9:86235800-86236200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
19	chr9:86235800-86236200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr9:86235800-86236200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr9:86235800-86236200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr9:86235800-86236200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr9:86235800-86236200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr9:86235800-86236200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr9:86235800-86236200	Enhancers	Adipose Nuclei	Adipose
26	chr9:86235800-86236200	Enhancers	Brain Cingulate Gyrus	brain
27	chr9:86235800-86236200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr9:86235800-86236200	Bivalent Enhancer	Placenta	Placenta
29	chr9:86235800-86236200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
30	chr9:86235800-86236200	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
31	chr9:86235800-86236200	Bivalent Enhancer	HUVEC	blood vessel
32	chr9:86235800-86236200	Enhancers	NHLF	lung
33	chr9:86235800-86236200	Flanking Active TSS	Osteobl	bone
34	chr9:86235800-86236400	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chr9:86235800-86236400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr9:86235800-86236600	Flanking Active TSS	Liver	Liver
37	chr9:86235800-86236800	Flanking Active TSS	HepG2	liver
38	chr9:86235800-86237400	Enhancers	Thymus	Thymus
39	chr9:86236000-86236200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr9:86236000-86236200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
41	chr9:86236000-86236200	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
42	chr9:86236000-86236200	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr9:86236000-86236200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr9:86236000-86236200	Enhancers	Primary T cells from cord blood	blood
45	chr9:86236000-86236200	Enhancers	Primary hematopoietic stem cells	blood
46	chr9:86236000-86236200	Enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr9:86236000-86236200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
48	chr9:86236000-86236200	Enhancers	Primary T helper cells PMA-I stimulated	--
49	chr9:86236000-86236200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr9:86236000-86236200	Enhancers	Cortex derived primary cultured neurospheres	brain

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