Variant report

Variant	rs2233800
Chromosome Location	chr9:19049057-19049058
allele	C/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	ATF3	chr9:19048911-19049452	A549	lung:	n/a	n/a
2	CTCF	chr9:19048987-19049321	MCF-7	breast:	n/a	chr9:19049165-19049178 chr9:19049162-19049180 chr9:19049164-19049185
3	YY1	chr9:19048932-19050155	GM12878	blood:	n/a	chr9:19049080-19049091 chr9:19049579-19049590 chr9:19049617-19049631 chr9:19049452-19049466
4	POLR2A	chr9:19048958-19049778	HUVEC	blood vessel:	n/a	n/a
5	EBF1	chr9:19049028-19049783	GM12878	blood:	n/a	n/a
6	RFX5	chr9:19048856-19049561	HepG2	liver:	n/a	chr9:19049204-19049219 chr9:19049207-19049216 chr9:19049205-19049219
7	MAX	chr9:19048713-19050204	HepG2	liver:	n/a	n/a
8	ZBTB33	chr9:19048832-19049746	SK-N-SH	brain:	n/a	chr9:19049356-19049366 chr9:19049358-19049367 chr9:19049359-19049369
9	POLR2A	chr9:19048930-19049662	A549	lung:	n/a	n/a
10	EP300	chr9:19048979-19049471	HepG2	liver:	n/a	chr9:19049374-19049381
11	CEBPB	chr9:19048966-19049375	H1-hESC	embryonic stem cell:	n/a	n/a
12	SMC3	chr9:19048802-19049817	Hela-S3	cervix:	n/a	chr9:19049164-19049178
13	TCF7L2	chr9:19049002-19049725	HCT-116	colon:	n/a	n/a
14	CTCF	chr9:19049010-19049341	GM12878	blood:	n/a	chr9:19049165-19049178 chr9:19049162-19049180 chr9:19049164-19049185
15	USF2	chr9:19048887-19049375	GM12878	blood:	n/a	n/a
16	POLR2A	chr9:19048867-19052986	Hela-S3	cervix:	n/a	n/a
17	NFIC	chr9:19048814-19050059	GM12878	blood:	n/a	n/a
18	POLR2A	chr9:19048837-19050536	GM19193	blood:	n/a	n/a
19	GABPA	chr9:19048930-19049883	A549	lung:	n/a	n/a
20	CTCF	chr9:19049040-19049190	AG04450	lung:	n/a	chr9:19049165-19049178 chr9:19049162-19049180 chr9:19049164-19049185
21	MXI1	chr9:19048918-19050208	Hela-S3	cervix:	n/a	chr9:19049201-19049216
22	RAD21	chr9:19048920-19049371	A549	lung:	n/a	chr9:19049167-19049176 chr9:19049166-19049179 chr9:19049075-19049088 chr9:19049163-19049182
23	POLR2A	chr9:19048849-19050253	GM12891	blood:	n/a	n/a
24	CTCF	chr9:19049037-19049315	K562	blood:	n/a	chr9:19049165-19049178 chr9:19049162-19049180 chr9:19049164-19049185
25	POLR2A	chr9:19048626-19050275	MCF10A-Er-Src	breast:	n/a	n/a
26	POLR2A	chr9:19048977-19049758	K562	blood:	n/a	n/a
27	POLR2A	chr9:19048860-19050025	GM12892	blood:	n/a	n/a
28	TAF1	chr9:19048704-19049635	ECC-1	luminal epithelium:	n/a	n/a
29	EP300	chr9:19048707-19049669	ECC-1	luminal epithelium:	n/a	chr9:19049540-19049556 chr9:19048854-19048868 chr9:19049374-19049381 chr9:19049537-19049553
30	YY1	chr9:19048969-19049474	HepG2	liver:	n/a	chr9:19049080-19049091 chr9:19049452-19049466
31	POU2F2	chr9:19048924-19049655	GM12891	blood:	n/a	chr9:19049588-19049600 chr9:19049383-19049395
32	TBP	chr9:19049011-19049597	K562	blood:	n/a	n/a
33	REST	chr9:19048456-19050673	H1-neurons	neurons:	n/a	chr9:19049531-19049544 chr9:19049550-19049563 chr9:19049514-19049532 chr9:19049631-19049649 chr9:19049553-19049566
34	HCFC1	chr9:19048511-19050417	Hela-S3	cervix:	n/a	n/a
35	YY1	chr9:19048961-19049872	GM12892	blood:	n/a	chr9:19049080-19049091 chr9:19049579-19049590 chr9:19049617-19049631 chr9:19049452-19049466
36	ETS1	chr9:19048999-19049680	GM12878	blood:	n/a	chr9:19049370-19049383 chr9:19049373-19049382 chr9:19049366-19049382 chr9:19049373-19049382 chr9:19049374-19049385 chr9:19049373-19049382 chr9:19049373-19049382 chr9:19049358-19049367 chr9:19049373-19049384 chr9:19049373-19049382 chr9:19049567-19049580 chr9:19049374-19049384
37	POLR2A	chr9:19048922-19049689	K562	blood:	n/a	n/a
38	EP300	chr9:19048994-19049454	SK-N-SH_RA	brain:	n/a	chr9:19049374-19049381
39	POLR2A	chr9:19048797-19050701	GM12892	blood:	n/a	n/a
40	MAX	chr9:19049002-19049649	A549	lung:	n/a	n/a
41	STAT5A	chr9:19048976-19049441	K562	blood:	n/a	n/a
42	FOXM1	chr9:19048787-19049779	GM12878	blood:	n/a	n/a
43	POLR2A	chr9:19048838-19050762	MCF-7	breast:	n/a	n/a
44	REST	chr9:19048874-19049964	A549	lung:	n/a	chr9:19049531-19049544 chr9:19049550-19049563 chr9:19049514-19049532 chr9:19049631-19049649 chr9:19049553-19049566
45	MYC	chr9:19048938-19049523	MCF-7	breast:	n/a	n/a
46	GABPA	chr9:19049054-19049580	Hela-S3	cervix:	n/a	n/a
47	YY1	chr9:19048933-19049841	A549	lung:	n/a	chr9:19049080-19049091 chr9:19049579-19049590 chr9:19049617-19049631 chr9:19049452-19049466
48	ATF2	chr9:19048920-19049758	GM12878	blood:	n/a	n/a
49	TCF12	chr9:19049029-19049415	A549	lung:	n/a	n/a
50	POLR2A	chr9:19048832-19049812	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:19048422..19049254-chr9:19457178..19458008,3	K562	blood:
2	chr9:19047624..19049710-chr9:19124952..19127835,2	MCF-7	breast:
3	chr9:19048660..19050563-chr9:19101012..19103938,3	MCF-7	breast:
4	chr9:19047048..19050954-chr9:19228997..19232024,5	K562	blood:
5	chr9:19048960..19051096-chr9:19378749..19380850,2	MCF-7	breast:
6	chr9:19049042..19049712-chrX:153284604..153285345,2	Hela-S3	cervix:
7	chr9:19047789..19050837-chr9:19378682..19381375,3	MCF-7	breast:
8	chr9:19048684..19049542-chr9:100684339..100685327,2	Hela-S3	cervix:
9	chr9:19047688..19050062-chr9:19125989..19129041,3	K562	blood:
10	chr9:19032362..19034123-chr9:19046838..19049376,2	MCF-7	breast:

Variant related genes	Relation type
RRAGA	TF binding region
ENSG00000147874	Chromatin interaction
ENSG00000184216	Chromatin interaction
ENSG00000147872	Chromatin interaction
ENSG00000155875	Chromatin interaction
ENSG00000137154	Chromatin interaction
ENSG00000136932	Chromatin interaction
ENSG00000137145	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10117419	1.00[ASN][1000 genomes]
rs10117445	1.00[ASN][1000 genomes]
rs10811096	0.85[EUR][1000 genomes]
rs10963937	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11496354	0.83[AMR][1000 genomes]
rs17236157	0.85[EUR][1000 genomes]
rs3177673	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4478656	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62560398	0.85[EUR][1000 genomes]
rs62560399	0.85[EUR][1000 genomes]
rs62560432	0.85[EUR][1000 genomes]
rs7858899	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs883440	0.85[EUR][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	nsv1017820	chr9:18882219-19587377	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
2	nsv540078	chr9:18882219-19587377	Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
3	nsv892700	chr9:18979441-19156784	Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv973452	chr9:19033958-19053096	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
5	nsv1028623	chr9:19034742-19394712	Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
6	nsv540079	chr9:19034742-19394712	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:19048000-19050600	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr9:19048200-19050400	Active TSS	HSMM	muscle
3	chr9:19048400-19049200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
4	chr9:19048400-19049200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr9:19048400-19049200	Flanking Active TSS	Stomach Smooth Muscle	stomach
6	chr9:19048400-19050000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr9:19048400-19050200	Active TSS	H1 Cell Line	embryonic stem cell
8	chr9:19048400-19050200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr9:19048400-19050400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr9:19048400-19050400	Active TSS	Colon Smooth Muscle	Colon
11	chr9:19048400-19050600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr9:19048400-19050600	Active TSS	Brain Anterior Caudate	brain
13	chr9:19048400-19050600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
14	chr9:19048400-19050800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr9:19048400-19050800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
16	chr9:19048400-19050800	Active TSS	A549	lung
17	chr9:19048400-19051000	Active TSS	Fetal Kidney	kidney
18	chr9:19048400-19051000	Active TSS	K562	blood
19	chr9:19048400-19051000	Active TSS	NHDF-Ad	bronchial
20	chr9:19048400-19051200	Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr9:19048400-19051200	Active TSS	H9 Cell Line	embryonic stem cell
22	chr9:19048400-19051200	Active TSS	Colonic Mucosa	Colon
23	chr9:19048400-19051200	Active TSS	Right Ventricle	heart
24	chr9:19048400-19051400	Active TSS	iPS-15b Cell Line	embryonic stem cell
25	chr9:19048400-19051600	Active TSS	iPS-18 Cell Line	embryonic stem cell
26	chr9:19048400-19051600	Active TSS	Pancreatic Islets	Pancreatic Islet
27	chr9:19048400-19051800	Active TSS	HUES48 Cell Line	embryonic stem cell
28	chr9:19048400-19051800	Active TSS	HUES6 Cell Line	embryonic stem cell
29	chr9:19048600-19049200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
30	chr9:19048600-19049200	Flanking Active TSS	Primary B cells from peripheral blood	blood
31	chr9:19048600-19049200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
32	chr9:19048600-19049200	Flanking Active TSS	Primary hematopoietic stem cells	blood
33	chr9:19048600-19049200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
34	chr9:19048600-19049200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
35	chr9:19048600-19049200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
36	chr9:19048600-19049200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr9:19048600-19049200	Flanking Active TSS	Fetal Thymus	thymus
38	chr9:19048600-19050400	Active TSS	iPS-20b Cell Line	embryonic stem cell
39	chr9:19048600-19050400	Active TSS	Fetal Brain Male	brain
40	chr9:19048600-19050600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr9:19048600-19050600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr9:19048600-19050600	Active TSS	Fetal Brain Female	brain
43	chr9:19048600-19050600	Bivalent/Poised TSS	HepG2	liver
44	chr9:19048600-19050600	Active TSS	HSMMtube	muscle
45	chr9:19048600-19050800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr9:19048600-19050800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr9:19048600-19050800	Active TSS	Sigmoid Colon	Sigmoid Colon
48	chr9:19048600-19050800	Active TSS	Thymus	Thymus
49	chr9:19048600-19051000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
50	chr9:19048600-19051000	Active TSS	Breast Myoepithelial Primary Cells	Breast

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