Variant report

Variant	rs16905568
Chromosome Location	chr9:98225469-98225470
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	MAZ	chr9:98224469-98225620	K562	blood:	n/a	chr9:98225514-98225524
2	POLR2A	chr9:98224585-98225555	SK-N-MC	brain:	n/a	n/a
3	RELA	chr9:98224675-98225506	GM19193	blood:	n/a	n/a
4	MAZ	chr9:98224465-98225741	GM12878	blood:	n/a	chr9:98225514-98225524
5	POLR2A	chr9:98224629-98225729	K562	blood:	n/a	n/a
6	RELA	chr9:98224567-98225634	GM18505	blood:	n/a	n/a
7	POLR2A	chr9:98224260-98226090	GM12878	blood:	n/a	n/a
8	POLR2A	chr9:98224688-98225487	K562	blood:	n/a	n/a
9	TBP	chr9:98224685-98225469	GM12878	blood:	n/a	n/a
10	POLR2A	chr9:98224686-98225814	GM19099	blood:	n/a	n/a
11	PAX5	chr9:98224468-98225650	GM12878	blood:	n/a	chr9:98225195-98225204 chr9:98224878-98224887
12	MYC	chr9:98224642-98225493	NB4	blood:	n/a	n/a
13	EP300	chr9:98224516-98225669	K562	blood:	n/a	chr9:98224875-98224889
14	BHLHE40	chr9:98224478-98225574	GM12878	blood:	n/a	n/a
15	NR2F2	chr9:98224614-98225547	K562	blood:	n/a	n/a
16	TAL1	chr9:98224730-98225485	K562	blood:	n/a	chr9:98225171-98225189 chr9:98224783-98224792
17	ZNF143	chr9:98224516-98225663	GM12878	blood:	n/a	n/a
18	TBL1XR1	chr9:98224501-98225480	GM12878	blood:	n/a	n/a
19	POLR2A	chr9:98224654-98226221	GM19193	blood:	n/a	n/a
20	TBP	chr9:98224615-98225529	K562	blood:	n/a	n/a
21	ZBTB7A	chr9:98224959-98225768	K562	blood:	n/a	n/a
22	RELA	chr9:98224523-98226061	GM10847	blood:	n/a	n/a
23	STAT5A	chr9:98224511-98225599	GM12878	blood:	n/a	chr9:98225551-98225562 chr9:98225051-98225063 chr9:98225267-98225279 chr9:98225511-98225523 chr9:98225283-98225295
24	MAZ	chr9:98224550-98226453	IMR90	lung:	n/a	chr9:98225514-98225524
25	CHD2	chr9:98224440-98225583	GM12878	blood:	n/a	chr9:98225271-98225281
26	POLR2A	chr9:98224726-98225544	K562	blood:	n/a	n/a
27	CUX1	chr9:98224652-98225548	K562	blood:	n/a	n/a
28	POLR2A	chr9:98224579-98225912	K562	blood:	n/a	n/a
29	MAX	chr9:98224569-98225506	NB4	blood:	n/a	n/a
30	MYC	chr9:98224687-98225518	K562	blood:	n/a	n/a
31	IRF1	chr9:98224842-98225497	K562	blood:	n/a	chr9:98224876-98224885
32	RCOR1	chr9:98224657-98225573	K562	blood:	n/a	n/a
33	POLR2A	chr9:98224635-98226057	GM18951	blood:	n/a	n/a
34	JUN	chr9:98224318-98225728	K562	blood:	n/a	n/a
35	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
36	POLR2A	chr9:98224439-98226044	GM12878	blood:	n/a	n/a
37	RELA	chr9:98224402-98225523	GM12878	blood:	n/a	n/a
38	IRF1	chr9:98224682-98225488	K562	blood:	n/a	chr9:98224876-98224885
39	RAD21	chr9:98224750-98225702	IMR90	lung:	n/a	n/a
40	MTA3	chr9:98224242-98225790	GM12878	blood:	n/a	n/a
41	POLR2A	chr9:98224195-98225950	GM12878	blood:	n/a	n/a
42	JUND	chr9:98224452-98225499	K562	blood:	n/a	n/a
43	RUNX3	chr9:98224423-98225667	GM12878	blood:	n/a	n/a
44	ZNF384	chr9:98224829-98225553	K562	blood:	n/a	n/a
45	GATA3	chr9:98224623-98225497	SK-N-SH	brain:	n/a	chr9:98225161-98225169 chr9:98225180-98225189 chr9:98225180-98225190 chr9:98225177-98225193 chr9:98225171-98225188 chr9:98225175-98225196
46	TCF12	chr9:98224469-98225485	SK-N-SH	brain:	n/a	n/a
47	CCNT2	chr9:98224778-98225492	K562	blood:	n/a	chr9:98225171-98225191 chr9:98225271-98225280
48	POLR2A	chr9:98224632-98225555	HL-60	blood:	n/a	n/a
49	MXI1	chr9:98224405-98225723	GM12878	blood:	n/a	n/a
50	TBL1XR1	chr9:98224759-98225494	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:98223864..98226761-chr9:98228381..98231062,3	K562	blood:
2	chr9:98223555..98229775-chr9:98269693..98275962,10	K562	blood:
3	chr9:98218910..98222494-chr9:98224731..98227835,5	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:

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

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

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12685109	1.00[AMR][1000 genomes]
rs16909877	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16912143	1.00[AMR][1000 genomes]
rs173339	1.00[JPT][hapmap]
rs2227970	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2765817	1.00[JPT][hapmap]
rs28522014	1.00[AMR][1000 genomes]
rs356663	1.00[JPT][hapmap]
rs356671	1.00[JPT][hapmap]
rs55758638	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55787302	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55986818	0.81[EUR][1000 genomes]
rs56222079	1.00[AMR][1000 genomes]
rs651009	1.00[JPT][hapmap]

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:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98206000-98237600	Weak transcription	Psoas Muscle	Psoas
2	chr9:98218800-98227400	Genic enhancers	Fetal Stomach	stomach
3	chr9:98221400-98226400	Genic enhancers	Fetal Intestine Small	intestine
4	chr9:98221800-98232400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr9:98223200-98226200	Genic enhancers	Fetal Intestine Large	intestine
6	chr9:98223400-98266400	Weak transcription	Hela-S3	cervix
7	chr9:98223600-98227600	Weak transcription	A549	lung
8	chr9:98224000-98225800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr9:98224000-98226200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr9:98224000-98226400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
11	chr9:98224000-98228800	Weak transcription	Liver	Liver
12	chr9:98224200-98225800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
13	chr9:98224200-98226200	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr9:98224200-98226200	Enhancers	Fetal Heart	heart
15	chr9:98224200-98227200	Weak transcription	Gastric	stomach
16	chr9:98224200-98227600	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr9:98224200-98228000	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr9:98224200-98228800	Weak transcription	Right Ventricle	heart
19	chr9:98224200-98229000	Weak transcription	Esophagus	oesophagus
20	chr9:98224400-98225800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
21	chr9:98224400-98225800	Flanking Active TSS	Fetal Thymus	thymus
22	chr9:98224400-98226000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr9:98224400-98226200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr9:98224400-98228800	Weak transcription	HepG2	liver
25	chr9:98224600-98225600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr9:98224600-98225600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr9:98224600-98225800	Genic enhancers	HUES48 Cell Line	embryonic stem cell
28	chr9:98224600-98225800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr9:98224600-98225800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
30	chr9:98224600-98225800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr9:98224600-98225800	Flanking Active TSS	Osteobl	bone
32	chr9:98224600-98226000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr9:98224600-98226200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr9:98224600-98226200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr9:98224600-98226200	Enhancers	iPS-15b Cell Line	embryonic stem cell
36	chr9:98224600-98226200	Enhancers	Placenta	Placenta
37	chr9:98224600-98226200	Enhancers	Sigmoid Colon	Sigmoid Colon
38	chr9:98224600-98226400	Enhancers	H1 Cell Line	embryonic stem cell
39	chr9:98224600-98226400	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr9:98224600-98226600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
41	chr9:98224600-98228800	Weak transcription	Aorta	Aorta
42	chr9:98224800-98225600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr9:98224800-98225600	Flanking Active TSS	Primary B cells from cord blood	blood
44	chr9:98224800-98225600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
45	chr9:98224800-98225600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
46	chr9:98224800-98225600	Active TSS	NHDF-Ad	bronchial
47	chr9:98224800-98225800	Flanking Active TSS	Fetal Muscle Leg	muscle
48	chr9:98224800-98226600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chr9:98225000-98225600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr9:98225000-98225600	Active TSS	Primary mononuclear cells fromperipheralblood	Blood

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