Variant report

Variant	rs9562961
Chromosome Location	chr13:50935841-50935842
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:50697261..50699908-chr13:50935542..50937568,2	K562	blood:
2	chr13:50698526..50701372-chr13:50933812..50935948,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DLEU7-9	chr13:50935546-50935899	NONHSAT033838

Variant related genes	Relation type
ENSG00000231607	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1149864	0.85[CHB][hapmap];0.86[JPT][hapmap];0.86[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];0.84[CHB][hapmap];0.89[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1269275	0.85[CHB][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs17074146	0.87[ASN][1000 genomes]
rs1924374	0.85[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs2240810	0.85[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.87[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];0.83[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]
rs9562963	0.83[AFR][1000 genomes]
rs9562969	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9568394	0.95[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs9568395	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]
rs9568396	0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs9568399	0.91[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv976114	chr13:50935447-50940164	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50930200-50939200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr13:50930200-50939600	Weak transcription	Duodenum Mucosa	Duodenum
3	chr13:50931600-50939000	Weak transcription	HepG2	liver
4	chr13:50932000-50940800	Weak transcription	Small Intestine	intestine
5	chr13:50932400-50936200	Enhancers	Primary T cells fromperipheralblood	blood
6	chr13:50932400-50936200	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr13:50932400-50936400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr13:50932800-50936200	Weak transcription	Fetal Brain Female	brain
9	chr13:50932800-50939400	Weak transcription	Gastric	stomach
10	chr13:50932800-50939400	Weak transcription	Pancreas	Pancrea
11	chr13:50932800-50939600	Weak transcription	Fetal Kidney	kidney
12	chr13:50933000-50936000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr13:50933200-50936600	Weak transcription	Fetal Heart	heart
14	chr13:50933200-50939200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr13:50933400-50939800	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr13:50933400-50944600	Weak transcription	Fetal Lung	lung
17	chr13:50933800-50944000	Weak transcription	Primary B cells from cord blood	blood
18	chr13:50934000-50939600	Weak transcription	Brain Germinal Matrix	brain
19	chr13:50934600-50936000	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr13:50934600-50942000	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr13:50935000-50936000	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr13:50935000-50939400	Weak transcription	Fetal Thymus	thymus
23	chr13:50935200-50936800	Enhancers	Liver	Liver
24	chr13:50935400-50936200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
25	chr13:50935600-50936200	Enhancers	Primary B cells from peripheral blood	blood
26	chr13:50935800-50936000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
27	chr13:50935800-50936200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr13:50935800-50936200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr13:50935800-50936200	Enhancers	Spleen	Spleen
30	chr13:50935800-50936400	Enhancers	Fetal Muscle Leg	muscle
31	chr13:50935800-50936400	Enhancers	Sigmoid Colon	Sigmoid Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links