Variant report

Variant	rs557254
Chromosome Location	chr15:55528012-55528013
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:55527245..55529399-chr15:55538940..55540733,2	K562	blood:
2	chr15:55527813..55534361-chr15:55567580..55576356,11	K562	blood:
3	chr15:55524035..55525892-chr15:55526403..55529147,3	K562	blood:
4	chr15:55526209..55528745-chr15:55538036..55540440,2	K562	blood:
5	chr15:55520811..55529435-chr15:55529925..55534726,12	K562	blood:
6	chr15:55526980..55531263-chr15:55533201..55537499,6	K562	blood:
7	chr15:55514943..55517401-chr15:55527045..55529673,2	K562	blood:
8	chr15:55488399..55490788-chr15:55526752..55530122,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000137876	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10518803	1.00[ASN][1000 genomes]
rs10518805	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12324754	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12324775	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12438278	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12439213	1.00[ASN][1000 genomes]
rs12439264	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12440497	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12440550	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12441258	1.00[ASN][1000 genomes]
rs12441307	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12442180	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12442887	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12442920	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12442937	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16976218	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16976220	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16976227	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16976229	0.90[EUR][1000 genomes]
rs16976231	0.90[EUR][1000 genomes]
rs17238178	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17238220	1.00[EUR][1000 genomes]
rs17819000	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17819012	0.80[EUR][1000 genomes]
rs28499877	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28705006	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61638549	1.00[ASN][1000 genomes]
rs7170936	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7171029	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7171897	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7173803	1.00[ASN][1000 genomes]
rs7177930	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8039254	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9920531	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]

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	nsv1043176	chr15:55010228-55563000	Genic enhancers Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1042741	chr15:55068022-55622497	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1039471	chr15:55137606-55552555	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv917323	chr15:55290499-56041334	Genic enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
5	nsv1043789	chr15:55400872-56092454	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
6	nsv1049977	chr15:55502508-55555694	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv1036924	chr15:55527874-55616480	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:55489800-55540200	Weak transcription	Esophagus	oesophagus
2	chr15:55490000-55529400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr15:55490000-55562800	Weak transcription	Ovary	ovary
4	chr15:55509400-55541600	Weak transcription	Small Intestine	intestine
5	chr15:55512800-55541600	Weak transcription	Colonic Mucosa	Colon
6	chr15:55513400-55532400	Weak transcription	Left Ventricle	heart
7	chr15:55514200-55532000	Weak transcription	Lung	lung
8	chr15:55514200-55532600	Weak transcription	Psoas Muscle	Psoas
9	chr15:55514200-55540400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr15:55514200-55545200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr15:55514400-55541200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr15:55514600-55534200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr15:55514600-55542600	Weak transcription	Hela-S3	cervix
14	chr15:55514600-55543200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr15:55514800-55532600	Weak transcription	Adipose Nuclei	Adipose
16	chr15:55514800-55539800	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr15:55514800-55560400	Weak transcription	Spleen	Spleen
18	chr15:55516000-55559600	Weak transcription	Fetal Stomach	stomach
19	chr15:55516200-55529400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr15:55517600-55542800	Weak transcription	Thymus	Thymus
21	chr15:55517800-55532400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr15:55517800-55539600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr15:55517800-55542200	Weak transcription	Fetal Thymus	thymus
24	chr15:55517800-55542800	Weak transcription	Primary B cells from peripheral blood	blood
25	chr15:55518000-55539200	Weak transcription	Fetal Lung	lung
26	chr15:55518600-55533600	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr15:55518600-55539400	Weak transcription	Placenta	Placenta
28	chr15:55518800-55541200	Weak transcription	Aorta	Aorta
29	chr15:55520800-55528400	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr15:55520800-55574800	Weak transcription	Stomach Smooth Muscle	stomach
31	chr15:55521000-55541400	Weak transcription	Fetal Intestine Large	intestine
32	chr15:55522400-55532400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr15:55522600-55529600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr15:55522800-55532400	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr15:55522800-55532600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr15:55522800-55534200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr15:55522800-55540600	Weak transcription	Liver	Liver
38	chr15:55522800-55543200	Weak transcription	Pancreas	Pancrea
39	chr15:55522800-55547000	Weak transcription	GM12878-XiMat	blood
40	chr15:55523200-55528200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr15:55523200-55542600	Weak transcription	HMEC	breast
42	chr15:55523400-55529600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr15:55523600-55533200	Weak transcription	Primary hematopoietic stem cells	blood
44	chr15:55524000-55531800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr15:55525400-55531800	Weak transcription	Gastric	stomach
46	chr15:55526600-55531600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr15:55526800-55529400	Weak transcription	Stomach Mucosa	stomach
48	chr15:55526800-55537200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr15:55526800-55543200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr15:55527000-55528200	Weak transcription	Rectal Mucosa Donor 31	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links