Variant report

Variant	rs10992250
Chromosome Location	chr9:94902575-94902576
allele	G/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	MAX	chr9:94902560-94903108	HCT-116	colon:	n/a	n/a
2	MAX	chr9:94902565-94903100	A549	lung:	n/a	n/a
3	MXI1	chr9:94902467-94903909	SK-N-SH	brain:	n/a	n/a
4	CTCF	chr9:94902444-94903129	HCT-116	colon:	n/a	chr9:94902742-94902755 chr9:94902741-94902762 chr9:94902739-94902757 chr9:94902740-94902756 chr9:94902739-94902752
5	RAD21	chr9:94902528-94902920	H1-hESC	embryonic stem cell:	n/a	chr9:94902741-94902755 chr9:94902740-94902759 chr9:94902741-94902750
6	RAD21	chr9:94902503-94903189	HCT-116	colon:	n/a	chr9:94902741-94902755 chr9:94902740-94902759 chr9:94902741-94902750
7	RAD21	chr9:94902517-94902971	ECC-1	luminal epithelium:	n/a	chr9:94902741-94902755 chr9:94902740-94902759 chr9:94902741-94902750
8	CTCF	chr9:94902475-94902934	A549	lung:	n/a	chr9:94902742-94902755 chr9:94902741-94902762 chr9:94902739-94902757 chr9:94902740-94902756 chr9:94902739-94902752
9	MYBL2	chr9:94902488-94902986	HepG2	liver:	n/a	n/a
10	CTCF	chr9:94902516-94902916	K562	blood:	n/a	chr9:94902742-94902755 chr9:94902741-94902762 chr9:94902739-94902757 chr9:94902740-94902756 chr9:94902739-94902752
11	MAX	chr9:94902556-94903030	H1-hESC	embryonic stem cell:	n/a	n/a
12	CTCF	chr9:94902533-94902970	H1-hESC	embryonic stem cell:	n/a	chr9:94902742-94902755 chr9:94902741-94902762 chr9:94902739-94902757 chr9:94902740-94902756 chr9:94902739-94902752
13	CTCF	chr9:94902530-94902911	GM12878	blood:	n/a	chr9:94902742-94902755 chr9:94902741-94902762 chr9:94902739-94902757 chr9:94902740-94902756 chr9:94902739-94902752
14	BCLAF1	chr9:94902534-94902978	GM12878	blood:	n/a	n/a
15	MAX	chr9:94902450-94903109	HCT-116	colon:	n/a	n/a
16	RAD21	chr9:94902562-94902954	GM12878	blood:	n/a	chr9:94902741-94902755 chr9:94902740-94902759 chr9:94902741-94902750
17	CTCF	chr9:94902487-94903061	MCF-7	breast:	n/a	chr9:94902742-94902755 chr9:94902741-94902762 chr9:94902739-94902757 chr9:94902740-94902756 chr9:94902739-94902752
18	MAZ	chr9:94902574-94902941	K562	blood:	n/a	n/a
19	CTCF	chr9:94902366-94902882	GM10266	blood:	n/a	chr9:94902742-94902755 chr9:94902741-94902762 chr9:94902739-94902757 chr9:94902740-94902756 chr9:94902739-94902752
20	RAD21	chr9:94902465-94902989	HepG2	liver:	n/a	chr9:94902741-94902755 chr9:94902740-94902759 chr9:94902741-94902750
21	RAD21	chr9:94902443-94903042	H1-hESC	embryonic stem cell:	n/a	chr9:94902741-94902755 chr9:94902740-94902759 chr9:94902741-94902750
22	CTCF	chr9:94902510-94902937	K562	blood:	n/a	chr9:94902742-94902755 chr9:94902741-94902762 chr9:94902739-94902757 chr9:94902740-94902756 chr9:94902739-94902752
23	SMC3	chr9:94902536-94902966	Hela-S3	cervix:	n/a	chr9:94902741-94902755 chr9:94902745-94902755
24	CBX3	chr9:94902536-94902959	K562	blood:	n/a	n/a
25	MAX	chr9:94902555-94903023	SK-N-SH	brain:	n/a	n/a
26	SIN3AK20	chr9:94902575-94903027	A549	lung:	n/a	n/a
27	MXI1	chr9:94902085-94904234	IMR90	lung:	n/a	n/a
28	RAD21	chr9:94902471-94903084	ECC-1	luminal epithelium:	n/a	chr9:94902741-94902755 chr9:94902740-94902759 chr9:94902741-94902750
29	CTCF	chr9:94902526-94902863	ECC-1	luminal epithelium:	n/a	chr9:94902742-94902755 chr9:94902741-94902762 chr9:94902739-94902757 chr9:94902740-94902756 chr9:94902739-94902752
30	CTCF	chr9:94902489-94903023	MCF-7	breast:	n/a	chr9:94902742-94902755 chr9:94902741-94902762 chr9:94902739-94902757 chr9:94902740-94902756 chr9:94902739-94902752
31	CTCF	chr9:94902554-94902863	HepG2	liver:	n/a	chr9:94902742-94902755 chr9:94902741-94902762 chr9:94902739-94902757 chr9:94902740-94902756 chr9:94902739-94902752
32	RAD21	chr9:94902512-94902980	HepG2	liver:	n/a	chr9:94902741-94902755 chr9:94902740-94902759 chr9:94902741-94902750
33	MAX	chr9:94902516-94903031	ECC-1	luminal epithelium:	n/a	n/a
34	RAD21	chr9:94902515-94903008	MCF-7	breast:	n/a	chr9:94902741-94902755 chr9:94902740-94902759 chr9:94902741-94902750
35	ZNF143	chr9:94902545-94902935	GM12878	blood:	n/a	chr9:94902900-94902915
36	YY1	chr9:94902572-94902919	GM12878	blood:	n/a	n/a
37	RAD21	chr9:94902486-94902985	A549	lung:	n/a	chr9:94902741-94902755 chr9:94902740-94902759 chr9:94902741-94902750
38	CTCF	chr9:94902340-94902971	IMR90	lung:	n/a	chr9:94902742-94902755 chr9:94902741-94902762 chr9:94902739-94902757 chr9:94902740-94902756 chr9:94902739-94902752
39	CTCF	chr9:94902534-94902909	A549	lung:	n/a	chr9:94902742-94902755 chr9:94902741-94902762 chr9:94902739-94902757 chr9:94902740-94902756 chr9:94902739-94902752
40	SMC3	chr9:94902569-94902945	K562	blood:	n/a	chr9:94902741-94902755 chr9:94902745-94902755
41	ZNF143	chr9:94902568-94902938	K562	blood:	n/a	chr9:94902900-94902915
42	FOXM1	chr9:94902503-94903072	GM12878	blood:	n/a	n/a
43	RAD21	chr9:94902303-94903113	SK-N-SH	brain:	n/a	chr9:94902741-94902755 chr9:94902740-94902759 chr9:94902741-94902750
44	CTCF	chr9:94902396-94902923	GM12892	blood:	n/a	chr9:94902742-94902755 chr9:94902741-94902762 chr9:94902739-94902757 chr9:94902740-94902756 chr9:94902739-94902752
45	E2F6	chr9:94902515-94903099	A549	lung:	n/a	chr9:94902748-94902759
46	MAX	chr9:94902561-94903071	H1-hESC	embryonic stem cell:	n/a	n/a
47	RAD21	chr9:94902540-94902939	HepG2	liver:	n/a	chr9:94902741-94902755 chr9:94902740-94902759 chr9:94902741-94902750
48	FOXA2	chr9:94902506-94902993	A549	lung:	n/a	n/a
49	TEAD4	chr9:94902499-94902906	HepG2	liver:	n/a	n/a
50	MAX	chr9:94902509-94903002	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:94900325..94903739-chr9:94909399..94912070,4	MCF-7	breast:
2	chr9:94902262..94903203-chr9:95396707..95397642,2	K562	blood:
3	chr9:94902342..94903195-chr9:95004476..95005483,4	MCF-7	breast:
4	chr9:94901685..94904988-chr9:95003695..95006795,3	MCF-7	breast:
5	chr9:94898906..94903668-chr9:95086648..95090271,5	MCF-7	breast:
6	chr9:94902503..94903236-chr9:95396725..95397397,2	MCF-7	breast:
7	chr9:94902223..94905302-chr9:94908199..94910430,4	MCF-7	breast:
8	chr9:94899946..94902668-chr9:94908231..94910049,3	K562	blood:
9	chr9:94902180..94903465-chr9:95004247..95005390,7	MCF-7	breast:

Variant related genes	Relation type
LINC00475	TF binding region
ENSG00000198000	Chromatin interaction
ENSG00000196305	Chromatin interaction
ENSG00000225511	Chromatin interaction
ENSG00000188312	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10820928	0.82[JPT][hapmap]
rs10820943	0.81[CEU][hapmap]
rs10992240	0.88[ASN][1000 genomes]
rs10992241	0.88[ASN][1000 genomes]
rs1970119	1.00[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.87[ASN][1000 genomes]
rs2398673	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs35121804	0.93[ASN][1000 genomes]
rs35814773	0.93[ASN][1000 genomes]
rs3858094	0.88[ASN][1000 genomes]
rs4391487	1.00[ASN][1000 genomes]
rs55667598	0.88[ASN][1000 genomes]
rs55801573	1.00[ASN][1000 genomes]
rs56319302	0.98[ASN][1000 genomes]
rs598843	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs62564361	0.93[ASN][1000 genomes]
rs62564363	0.93[ASN][1000 genomes]
rs62564364	0.93[ASN][1000 genomes]
rs62568697	0.88[ASN][1000 genomes]
rs7044976	0.87[CEU][hapmap]
rs72748370	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7465866	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949008	chr9:94500776-95182133	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1050845	chr9:94687959-95312406	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv1046733	chr9:94690622-95138564	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv530947	chr9:94697309-95093377	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv917089	chr9:94857047-95099848	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv969760	chr9:94877924-94966209	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
7	nsv893572	chr9:94891778-94944778	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv972778	chr9:94902068-94908273	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10992250	ZNF484	cis	parietal	SCAN
rs10992250	CENPP	cis	cerebellum	SCAN
rs10992250	SPTLC1	cis	parietal	SCAN
rs10992250	ZNF484	cis	cerebellum	SCAN
rs10992250	FANCC	cis	cerebellum	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94896600-94902800	Weak transcription	Gastric	stomach
2	chr9:94896800-94902600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr9:94896800-94902800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr9:94896800-94902800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr9:94896800-94902800	Weak transcription	Esophagus	oesophagus
6	chr9:94896800-94902800	Weak transcription	Right Atrium	heart
7	chr9:94896800-94902800	Weak transcription	A549	lung
8	chr9:94897200-94902800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr9:94897200-94902800	Weak transcription	HUVEC	blood vessel
10	chr9:94897400-94902800	Weak transcription	NHDF-Ad	bronchial
11	chr9:94897600-94902800	Weak transcription	HMEC	breast
12	chr9:94900000-94903000	Flanking Active TSS	HepG2	liver
13	chr9:94900200-94902600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr9:94900200-94902600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr9:94900200-94903200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr9:94900400-94902800	Weak transcription	Hela-S3	cervix
17	chr9:94900400-94902800	Weak transcription	K562	blood
18	chr9:94900600-94902600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr9:94900800-94902600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr9:94900800-94902600	Weak transcription	Dnd41	blood
21	chr9:94900800-94903000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr9:94900800-94903000	Enhancers	HSMMtube	muscle
23	chr9:94901000-94902800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr9:94901600-94902800	Weak transcription	NH-A	brain
25	chr9:94902000-94903000	Enhancers	NHLF	lung
26	chr9:94902200-94902800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr9:94902200-94902800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr9:94902200-94902800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr9:94902200-94902800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
30	chr9:94902200-94902800	Enhancers	HSMM	muscle
31	chr9:94902200-94903000	Enhancers	Placenta	Placenta
32	chr9:94902200-94903200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr9:94902200-94904200	Enhancers	Liver	Liver
34	chr9:94902400-94902600	Enhancers	HUES6 Cell Line	embryonic stem cell
35	chr9:94902400-94902600	Bivalent Enhancer	Stomach Smooth Muscle	stomach
36	chr9:94902400-94902800	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr9:94902400-94902800	Enhancers	Primary B cells from peripheral blood	blood
38	chr9:94902400-94902800	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
39	chr9:94902400-94902800	Enhancers	Muscle Satellite Cultured Cells	--
40	chr9:94902400-94902800	Enhancers	Colonic Mucosa	Colon
41	chr9:94902400-94902800	Enhancers	Duodenum Smooth Muscle	Duodenum
42	chr9:94902400-94902800	Enhancers	Ovary	ovary
43	chr9:94902400-94902800	Enhancers	Pancreas	Pancrea
44	chr9:94902400-94902800	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
45	chr9:94902400-94902800	Enhancers	Osteobl	bone
46	chr9:94902400-94903000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
47	chr9:94902400-94903000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr9:94902400-94903000	Enhancers	Placenta Amnion	Placenta Amnion
49	chr9:94902400-94903000	Enhancers	Spleen	Spleen
50	chr9:94902400-94903200	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links