Variant report

Variant	rs28698995
Chromosome Location	chr9:98224487-98224488
allele	C/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	MAZ	chr9:98224469-98225620	K562	blood:	n/a	chr9:98225514-98225524
2	MAZ	chr9:98224465-98225741	GM12878	blood:	n/a	chr9:98225514-98225524
3	POLR2A	chr9:98224260-98226090	GM12878	blood:	n/a	n/a
4	NFIC	chr9:98224460-98225240	GM12878	blood:	n/a	n/a
5	PAX5	chr9:98224468-98225650	GM12878	blood:	n/a	chr9:98225195-98225204 chr9:98224878-98224887
6	NFYB	chr9:98224386-98225260	K562	blood:	n/a	n/a
7	BHLHE40	chr9:98224478-98225574	GM12878	blood:	n/a	n/a
8	RELA	chr9:98224347-98225280	GM19099	blood:	n/a	n/a
9	CUX1	chr9:98224409-98225237	GM12878	blood:	n/a	n/a
10	CHD2	chr9:98224440-98225583	GM12878	blood:	n/a	chr9:98225271-98225281
11	EP300	chr9:98224437-98225282	GM12878	blood:	n/a	chr9:98224875-98224889
12	JUN	chr9:98224318-98225728	K562	blood:	n/a	n/a
13	GATA1	chr9:98224155-98225483	K562	blood:	n/a	chr9:98225161-98225169 chr9:98225180-98225189 chr9:98225180-98225190 chr9:98225177-98225193 chr9:98225171-98225188 chr9:98225175-98225196
14	POLR2A	chr9:98224439-98226044	GM12878	blood:	n/a	n/a
15	CHD1	chr9:98224386-98225214	GM12878	blood:	n/a	n/a
16	RELA	chr9:98224402-98225523	GM12878	blood:	n/a	n/a
17	MTA3	chr9:98224242-98225790	GM12878	blood:	n/a	n/a
18	POLR2A	chr9:98224195-98225950	GM12878	blood:	n/a	n/a
19	NFIC	chr9:98224377-98225349	GM12878	blood:	n/a	n/a
20	TEAD4	chr9:98224413-98225424	K562	blood:	n/a	n/a
21	JUND	chr9:98224452-98225499	K562	blood:	n/a	n/a
22	RUNX3	chr9:98224423-98225667	GM12878	blood:	n/a	n/a
23	FOXM1	chr9:98224392-98225299	GM12878	blood:	n/a	n/a
24	TCF12	chr9:98224469-98225485	SK-N-SH	brain:	n/a	n/a
25	MXI1	chr9:98224405-98225723	GM12878	blood:	n/a	n/a
26	GATA1	chr9:98224359-98225283	PBDE	blood:	n/a	chr9:98225161-98225169 chr9:98225180-98225189 chr9:98225180-98225190 chr9:98225177-98225193 chr9:98225171-98225188 chr9:98225175-98225196
27	ATF2	chr9:98224457-98225273	GM12878	blood:	n/a	n/a
28	EBF1	chr9:98224434-98225330	GM12878	blood:	n/a	n/a
29	RCOR1	chr9:98224262-98225400	K562	blood:	n/a	n/a
30	MXI1	chr9:98224420-98225943	IMR90	lung:	n/a	n/a
31	RUNX3	chr9:98224379-98225678	GM12878	blood:	n/a	n/a
32	EP300	chr9:98224410-98225317	GM12878	blood:	n/a	chr9:98224875-98224889
33	POLR2A	chr9:98224144-98226168	GM12878	blood:	n/a	n/a
34	TRIM28	chr9:98224482-98225415	K562	blood:	n/a	n/a
35	MAX	chr9:98224402-98225710	K562	blood:	n/a	chr9:98225514-98225524
36	CBX3	chr9:98224396-98225508	K562	blood:	n/a	n/a
37	TBL1XR1	chr9:98224403-98225496	K562	blood:	n/a	n/a
38	POLR2A	chr9:98224335-98226055	GM12891	blood:	n/a	n/a
39	FOXM1	chr9:98224444-98225332	GM12878	blood:	n/a	n/a
40	RELA	chr9:98224400-98225798	GM12891	blood:	n/a	n/a
41	SP1	chr9:98224452-98225251	GM12878	blood:	n/a	chr9:98225077-98225091 chr9:98225049-98225058

No.	Distal block	Cell Line	Cell type
1	chr9:98222888..98225027-chr9:98277335..98280257,3	K562	blood:
2	chr9:98223864..98226761-chr9:98228381..98231062,3	K562	blood:
3	chr9:98223555..98229775-chr9:98269693..98275962,10	K562	blood:
4	chr9:98222977..98229750-chr9:98267050..98274823,12	K562	blood:
5	chr12:53297243..53298949-chr9:98222802..98225552,2	MCF-7	breast:
6	chr9:98223412..98227347-chr9:98253313..98257210,3	K562	blood:
7	chr9:98223181..98225027-chr9:98277335..98280257,2	K562	blood:

Variant related genes	Relation type
PTCH1	TF binding region
ENSG00000185920	Chromatin interaction
ENSG00000271314	Chromatin interaction
ENSG00000271155	Chromatin interaction
ENSG00000170421	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs2282040	0.80[AFR][1000 genomes]
rs28390100	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28429270	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28441412	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28474857	0.80[AFR][1000 genomes]
rs28583690	0.89[AFR][1000 genomes]
rs28601668	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28673156	0.80[AFR][1000 genomes]
rs28676757	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531633	chr9:98078300-98431120	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv831658	chr9:98152971-98342178	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv949520	chr9:98204199-98238358	Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv430083	chr9:98204245-98445645	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv1053762	chr9:98208542-98232120	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv1047465	chr9:98217524-98228225	Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 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	chr9:98202000-98224600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr9:98206000-98237600	Weak transcription	Psoas Muscle	Psoas
3	chr9:98206600-98224600	Strong transcription	Aorta	Aorta
4	chr9:98206600-98225200	Strong transcription	Pancreas	Pancrea
5	chr9:98211400-98224600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr9:98212000-98224600	Strong transcription	Skeletal Muscle Female	skeletal muscle
7	chr9:98213200-98224600	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr9:98214200-98225400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr9:98215200-98224600	Weak transcription	Osteobl	bone
10	chr9:98218800-98227400	Genic enhancers	Fetal Stomach	stomach
11	chr9:98219400-98225400	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr9:98219800-98224600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr9:98220000-98224600	Genic enhancers	Fetal Lung	lung
14	chr9:98220200-98225000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr9:98220600-98224600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr9:98221200-98224600	Genic enhancers	Fetal Muscle Leg	muscle
17	chr9:98221400-98226400	Genic enhancers	Fetal Intestine Small	intestine
18	chr9:98221600-98224600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr9:98221800-98224600	Weak transcription	Placenta	Placenta
20	chr9:98221800-98232400	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr9:98222000-98224800	Enhancers	Fetal Brain Female	brain
22	chr9:98222200-98224600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr9:98222200-98224600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr9:98222800-98224600	Enhancers	Brain Germinal Matrix	brain
25	chr9:98223000-98224600	Strong transcription	H9 Cell Line	embryonic stem cell
26	chr9:98223000-98224600	Genic enhancers	Sigmoid Colon	Sigmoid Colon
27	chr9:98223200-98224600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr9:98223200-98224600	Genic enhancers	Rectal Mucosa Donor 29	rectum
29	chr9:98223200-98224600	Weak transcription	Rectal Smooth Muscle	rectum
30	chr9:98223200-98226200	Genic enhancers	Fetal Intestine Large	intestine
31	chr9:98223400-98224600	Genic enhancers	HUES6 Cell Line	embryonic stem cell
32	chr9:98223400-98224600	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr9:98223400-98224600	Genic enhancers	Rectal Mucosa Donor 31	rectum
34	chr9:98223400-98224800	Weak transcription	Ovary	ovary
35	chr9:98223400-98266400	Weak transcription	Hela-S3	cervix
36	chr9:98223600-98224600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr9:98223600-98224600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
38	chr9:98223600-98224800	Enhancers	Duodenum Smooth Muscle	Duodenum
39	chr9:98223600-98227600	Weak transcription	A549	lung
40	chr9:98223800-98224600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr9:98223800-98224600	Enhancers	Primary T helper cells PMA-I stimulated	--
42	chr9:98223800-98224600	Enhancers	Colonic Mucosa	Colon
43	chr9:98224000-98224600	Enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr9:98224000-98224600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
45	chr9:98224000-98224600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr9:98224000-98224600	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
47	chr9:98224000-98224600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
48	chr9:98224000-98224600	Strong transcription	Stomach Mucosa	stomach
49	chr9:98224000-98225000	Flanking Active TSS	Primary T cells from cord blood	blood
50	chr9:98224000-98225400	Enhancers	Primary hematopoietic stem cells	blood

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