Variant report

Variant	rs9584575
Chromosome Location	chr13:98084675-98084676
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	RCOR1	chr13:98084635-98086504	IMR90	lung:	n/a	n/a
2	POLR2A	chr13:98084527-98087335	H1-hESC	embryonic stem cell:	n/a	n/a
3	RELA	chr13:98084570-98086193	GM19099	blood:	n/a	n/a
4	CHD1	chr13:98084629-98085170	GM12878	blood:	n/a	n/a
5	SPI1	chr13:98084520-98084730	GM12891	blood:	n/a	chr13:98084642-98084655
6	POLR2A	chr13:98084510-98087400	GM19099	blood:	n/a	n/a
7	POLR2A	chr13:98084594-98086327	SK-N-SH	brain:	n/a	n/a
8	CHD1	chr13:98084569-98086399	IMR90	lung:	n/a	n/a
9	REST	chr13:98084393-98087806	H1-neurons	neurons:	n/a	chr13:98085145-98085163 chr13:98085340-98085353
10	POLR2A	chr13:98084565-98087399	GM12892	blood:	n/a	n/a
11	CHD2	chr13:98084646-98086472	GM12878	blood:	n/a	n/a
12	RFX5	chr13:98083186-98086694	SK-N-SH	brain:	n/a	chr13:98085517-98085531 chr13:98085516-98085531
13	WRNIP1	chr13:98084668-98086135	GM12878	blood:	n/a	n/a
14	EP300	chr13:98084544-98086187	GM12878	blood:	n/a	chr13:98085977-98085990
15	POLR2A	chr13:98084412-98087756	GM12891	blood:	n/a	n/a
16	TBP	chr13:98084631-98086215	GM12878	blood:	n/a	n/a
17	POLR2A	chr13:98084524-98087560	GM18951	blood:	n/a	n/a
18	POLR2A	chr13:98084604-98086313	U87	brain:	n/a	n/a
19	POLR2A	chr13:98084580-98087116	NB4	blood:	n/a	n/a
20	SPI1	chr13:98084458-98084815	GM12878	blood:	n/a	chr13:98084642-98084655
21	RELA	chr13:98084586-98086584	GM15510	blood:	n/a	n/a
22	MAX	chr13:98084525-98086415	NB4	blood:	n/a	chr13:98085402-98085415 chr13:98085403-98085414 chr13:98085404-98085413 chr13:98085402-98085415 chr13:98085405-98085412 chr13:98085404-98085413 chr13:98085403-98085413 chr13:98085403-98085413 chr13:98085403-98085414 chr13:98085402-98085412 chr13:98085403-98085414 chr13:98085402-98085415
23	RELA	chr13:98084591-98086233	GM18951	blood:	n/a	n/a
24	POLR2A	chr13:98084476-98086323	U87	brain:	n/a	n/a
25	POLR2A	chr13:98084613-98086317	U87	brain:	n/a	n/a
26	MAZ	chr13:98084500-98087858	IMR90	lung:	n/a	chr13:98085402-98085415 chr13:98085403-98085414 chr13:98085404-98085413 chr13:98085402-98085415 chr13:98085405-98085412 chr13:98085404-98085413 chr13:98085403-98085413 chr13:98085403-98085413 chr13:98085403-98085414 chr13:98087298-98087307 chr13:98085403-98085414 chr13:98085402-98085415
27	CREB1	chr13:98084625-98086337	GM12878	blood:	n/a	n/a
28	MXI1	chr13:98084522-98086576	GM12878	blood:	n/a	n/a
29	MAX	chr13:98084466-98086525	A549	lung:	n/a	chr13:98085402-98085415 chr13:98085403-98085414 chr13:98085404-98085413 chr13:98085402-98085415 chr13:98085405-98085412 chr13:98085404-98085413 chr13:98085403-98085413 chr13:98085403-98085413 chr13:98085403-98085414 chr13:98085402-98085412 chr13:98085403-98085414 chr13:98085402-98085415
30	POLR2A	chr13:98084554-98087527	GM12878	blood:	n/a	n/a
31	MYC	chr13:98084629-98087393	NB4	blood:	n/a	chr13:98085402-98085415 chr13:98085403-98085414 chr13:98085404-98085413 chr13:98085402-98085415 chr13:98085405-98085412 chr13:98085404-98085413 chr13:98085403-98085413 chr13:98085403-98085413 chr13:98085403-98085414 chr13:98087298-98087307 chr13:98085402-98085412 chr13:98085403-98085414 chr13:98085402-98085415
32	EP300	chr13:98084519-98084880	GM12878	blood:	n/a	n/a
33	POLR2A	chr13:98084593-98086794	HUVEC	blood vessel:	n/a	n/a
34	POLR2A	chr13:98084581-98086317	PBDE	blood:	n/a	n/a
35	POLR2A	chr13:98084576-98087378	GM18505	blood:	n/a	n/a
36	POLR2A	chr13:98084510-98087268	Raji	blood:	n/a	n/a
37	SIN3A	chr13:98084588-98086506	H1-hESC	embryonic stem cell:	n/a	n/a
38	MYC	chr13:98084604-98085609	H1-hESC	embryonic stem cell:	n/a	chr13:98085402-98085415 chr13:98085403-98085414 chr13:98085404-98085413 chr13:98085402-98085415 chr13:98085405-98085412 chr13:98085404-98085413 chr13:98085403-98085413 chr13:98085403-98085413 chr13:98085403-98085414 chr13:98085402-98085412 chr13:98085403-98085414 chr13:98085402-98085415
39	RFX5	chr13:98084426-98086613	IMR90	lung:	n/a	chr13:98085517-98085531 chr13:98085516-98085531
40	MXI1	chr13:98084370-98087869	SK-N-SH	brain:	n/a	n/a
41	MAX	chr13:98084613-98086290	GM12878	blood:	n/a	chr13:98085402-98085415 chr13:98085403-98085414 chr13:98085404-98085413 chr13:98085402-98085415 chr13:98085405-98085412 chr13:98085404-98085413 chr13:98085403-98085413 chr13:98085403-98085413 chr13:98085403-98085414 chr13:98085402-98085412 chr13:98085403-98085414 chr13:98085402-98085415
42	POLR2A	chr13:98084622-98087254	GM15510	blood:	n/a	n/a
43	BHLHE40	chr13:98084588-98086514	GM12878	blood:	n/a	chr13:98085193-98085209
44	EP300	chr13:98083473-98087710	SK-N-SH	brain:	n/a	chr13:98086667-98086676 chr13:98085977-98085990
45	STAT1	chr13:98084658-98086317	GM12878	blood:	n/a	chr13:98085177-98085189 chr13:98084845-98084857
46	TBL1XR1	chr13:98084674-98086230	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:98078675..98081221-chr13:98083499..98086151,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-OXGR1-6	chr13:98081597-98086236	NONHSAT034832

Variant related genes	Relation type
RAP2A	TF binding region

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10161600	1.00[EUR][1000 genomes]
rs10161693	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12100323	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12100327	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13378123	0.92[EUR][1000 genomes]
rs13378459	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13378500	0.92[EUR][1000 genomes]
rs13378554	0.92[EUR][1000 genomes]
rs13378832	0.92[EUR][1000 genomes]
rs13378938	0.92[EUR][1000 genomes]
rs55935003	0.92[EUR][1000 genomes]
rs7318655	1.00[MEX][hapmap]
rs74105181	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9300411	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs9300412	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9300413	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9300414	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9582131	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs9582133	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs9582135	1.00[ASW][hapmap];0.83[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9582137	0.87[AMR][1000 genomes]
rs9584567	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9584570	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9584572	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs9584573	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs9584574	1.00[EUR][1000 genomes]
rs9584576	1.00[EUR][1000 genomes]
rs9584577	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9584578	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9584579	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs9584580	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9584581	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9584583	0.83[GIH][hapmap];1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832694	chr13:97930561-98137882	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	esv1791802	chr13:98076911-98096882	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	esv1804050	chr13:98076911-98096882	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	esv1794802	chr13:98076911-98106042	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	esv1797132	chr13:98076911-98106042	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv562794	chr13:98083262-98086828	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
7	nsv562795	chr13:98084675-98086470	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:98076400-98084800	Weak transcription	Esophagus	oesophagus
2	chr13:98082200-98085000	Weak transcription	K562	blood
3	chr13:98082400-98084800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr13:98082800-98084800	Weak transcription	Spleen	Spleen
5	chr13:98083200-98088000	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr13:98083400-98088800	Active TSS	GM12878-XiMat	blood
7	chr13:98083600-98084800	Flanking Active TSS	Dnd41	blood
8	chr13:98083600-98088200	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr13:98083800-98084800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr13:98083800-98088600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr13:98083800-98089200	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr13:98084000-98088000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr13:98084000-98088600	Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr13:98084000-98088800	Active TSS	iPS-20b Cell Line	embryonic stem cell
15	chr13:98084000-98088800	Active TSS	Fetal Kidney	kidney
16	chr13:98084000-98089200	Active TSS	NHLF	lung
17	chr13:98084200-98084800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr13:98084200-98085200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr13:98084200-98088000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr13:98084200-98088000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr13:98084200-98088000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr13:98084200-98088200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr13:98084200-98089000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr13:98084200-98089000	Active TSS	NHDF-Ad	bronchial
25	chr13:98084400-98084800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
26	chr13:98084400-98084800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
27	chr13:98084400-98084800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
28	chr13:98084400-98084800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
29	chr13:98084400-98084800	Flanking Active TSS	Fetal Heart	heart
30	chr13:98084400-98084800	Flanking Active TSS	Fetal Intestine Small	intestine
31	chr13:98084400-98084800	Flanking Active TSS	Stomach Smooth Muscle	stomach
32	chr13:98084400-98084800	Flanking Active TSS	NH-A	brain
33	chr13:98084400-98085000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
34	chr13:98084400-98085000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
35	chr13:98084400-98085000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
36	chr13:98084400-98085000	Flanking Active TSS	Fetal Lung	lung
37	chr13:98084400-98085000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
38	chr13:98084400-98085000	Flanking Active TSS	HUVEC	blood vessel
39	chr13:98084400-98085200	Flanking Active TSS	Primary hematopoietic stem cells	blood
40	chr13:98084400-98085200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
41	chr13:98084400-98085200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr13:98084400-98085200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
43	chr13:98084400-98085200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
44	chr13:98084400-98085200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
45	chr13:98084400-98087200	Active TSS	Primary T helper naive cells from peripheral blood	blood
46	chr13:98084400-98087600	Active TSS	HUES64 Cell Line	embryonic stem cell
47	chr13:98084400-98087600	Active TSS	A549	lung
48	chr13:98084400-98088000	Active TSS	Duodenum Mucosa	Duodenum
49	chr13:98084400-98088000	Active TSS	Rectal Smooth Muscle	rectum
50	chr13:98084400-98088200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links