Variant report

Variant	rs9568395
Chromosome Location	chr13:50940761-50940762
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	EP300	chr13:50940633-50940986	SK-N-SH_RA	brain:	n/a	n/a
2	FOXA2	chr13:50940154-50940853	A549	lung:	n/a	n/a
3	FOXM1	chr13:50940735-50941407	GM12878	blood:	n/a	n/a
4	MTA3	chr13:50940690-50941460	GM12878	blood:	n/a	n/a
5	NFIC	chr13:50940529-50941087	SK-N-SH	brain:	n/a	chr13:50940793-50940821 chr13:50940804-50940821
6	EBF1	chr13:50940735-50941302	GM12878	blood:	n/a	n/a
7	TCF12	chr13:50939700-50940805	A549	lung:	n/a	chr13:50940173-50940180
8	FOXM1	chr13:50940744-50941423	GM12878	blood:	n/a	n/a
9	STAT5A	chr13:50940706-50941383	GM12878	blood:	n/a	n/a
10	RUNX3	chr13:50940758-50941459	GM12878	blood:	n/a	n/a
11	STAT1	chr13:50940731-50940824	GM12878	blood:	n/a	n/a
12	GATA3	chr13:50940719-50940978	SH-SY5Y	brain:	n/a	n/a
13	NFIC	chr13:50940729-50941401	GM12878	blood:	n/a	chr13:50940793-50940821 chr13:50940804-50940821
14	GATA2	chr13:50940445-50941205	SH-SY5Y	brain:	n/a	n/a
15	FOXA2	chr13:50939862-50940831	A549	lung:	n/a	n/a
16	RUNX3	chr13:50940695-50941458	GM12878	blood:	n/a	n/a
17	ATF2	chr13:50940698-50941406	GM12878	blood:	n/a	n/a
18	GATA3	chr13:50939849-50940831	A549	lung:	n/a	chr13:50940144-50940153
19	NFIC	chr13:50940745-50941440	GM12878	blood:	n/a	chr13:50940793-50940821 chr13:50940804-50940821
20	GATA3	chr13:50939818-50940830	MCF-7	breast:	n/a	chr13:50940144-50940153
21	EP300	chr13:50939575-50941676	SK-N-SH	brain:	n/a	chr13:50940142-50940151

No.	Distal block	Cell Line	Cell type
1	chr13:50931295..50934143-chr13:50939870..50941977,3	MCF-7	breast:
2	chr13:50698177..50699740-chr13:50938730..50941309,2	MCF-7	breast:
3	chr13:50929441..50932225-chr13:50939480..50941358,2	MCF-7	breast:
4	chr13:50939370..50941845-chr13:50950043..50952232,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000221198	TF binding region
RPL34P26	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1149864	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs1149869	0.85[ASN][1000 genomes]
rs12428570	0.87[AMR][1000 genomes]
rs12430306	0.87[AMR][1000 genomes]
rs1269265	1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1269275	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs17074146	0.86[ASN][1000 genomes]
rs1924374	0.90[CHB][hapmap];0.86[ASN][1000 genomes]
rs2240810	0.90[CHB][hapmap];0.86[ASN][1000 genomes]
rs2532968	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35824953	0.83[AFR][1000 genomes]
rs806305	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs806309	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs806348	0.85[EUR][1000 genomes]
rs806354	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs806356	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs811714	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9535442	0.87[ASN][1000 genomes]
rs9535444	0.87[ASN][1000 genomes]
rs9562961	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9562963	0.83[AFR][1000 genomes]
rs9562969	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9568394	1.00[CHB][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]
rs9568396	1.00[CHB][hapmap];0.89[JPT][hapmap];0.98[ASN][1000 genomes]
rs9568399	0.91[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035151	chr13:50513535-51167850	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1254 gene(s)	inside rSNPs	diseases
2	esv2753964	chr13:50545399-51421199	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
3	esv2753492	chr13:50550081-51461720	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
4	esv2752608	chr13:50550099-51054499	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1249 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50932000-50940800	Weak transcription	Small Intestine	intestine
2	chr13:50933400-50944600	Weak transcription	Fetal Lung	lung
3	chr13:50933800-50944000	Weak transcription	Primary B cells from cord blood	blood
4	chr13:50934600-50942000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr13:50937000-50940800	Weak transcription	Fetal Heart	heart
6	chr13:50939200-50941400	Enhancers	Stomach Mucosa	stomach
7	chr13:50939400-50940800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
8	chr13:50939400-50940800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
9	chr13:50939400-50941200	Enhancers	Rectal Mucosa Donor 31	rectum
10	chr13:50939400-50941400	Enhancers	Primary B cells from peripheral blood	blood
11	chr13:50939400-50942000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr13:50939600-50940800	Flanking Active TSS	GM12878-XiMat	blood
13	chr13:50939600-50941000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
14	chr13:50939600-50941000	Enhancers	Brain Germinal Matrix	brain
15	chr13:50939600-50941200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr13:50939800-50940800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
17	chr13:50939800-50940800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
18	chr13:50939800-50940800	Enhancers	Muscle Satellite Cultured Cells	--
19	chr13:50939800-50940800	Flanking Active TSS	HUVEC	blood vessel
20	chr13:50939800-50941000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
21	chr13:50939800-50941000	Weak transcription	Gastric	stomach
22	chr13:50939800-50953400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr13:50940000-50940800	Active TSS	Rectal Mucosa Donor 29	rectum
24	chr13:50940000-50941000	Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr13:50940000-50941000	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr13:50940200-50941000	Enhancers	HepG2	liver
27	chr13:50940200-50952600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr13:50940400-50940800	Enhancers	Osteobl	bone
29	chr13:50940400-50941000	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr13:50940400-50941000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr13:50940400-50941200	Enhancers	Fetal Intestine Small	intestine
32	chr13:50940400-50942000	Enhancers	Primary T cells fromperipheralblood	blood
33	chr13:50940600-50940800	Flanking Active TSS	A549	lung
34	chr13:50940600-50941000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr13:50940600-50941400	Enhancers	Liver	Liver
36	chr13:50940600-50941400	Enhancers	Duodenum Mucosa	Duodenum
37	chr13:50940600-50941400	Enhancers	Fetal Kidney	kidney
38	chr13:50940600-50941600	Enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr13:50940600-50942000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr13:50940600-50942400	Enhancers	Primary T helper cells fromperipheralblood	blood

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