Variant report

Variant	rs12442887
Chromosome Location	chr15:55512455-55512456
allele	A/G
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:55506823..55512825-chr15:55581621..55584797,8	K562	blood:
2	chr15:55491408..55493022-chr15:55511973..55513991,2	K562	blood:
3	chr15:55506823..55513814-chr15:55580257..55584341,9	K562	blood:
4	chr15:55510048..55513584-chr15:55529255..55531820,4	K562	blood:
5	chr15:55504661..55507549-chr15:55511770..55516084,4	K562	blood:
6	chr15:55507731..55513408-chr15:55580265..55584053,9	MCF-7	breast:
7	chr15:55485223..55489171-chr15:55508275..55513421,7	K562	blood:
8	chr15:55508422..55515195-chr15:55580692..55586566,10	MCF-7	breast:
9	chr15:55511874..55516207-chr15:55570260..55572623,4	K562	blood:
10	chr15:55507956..55509832-chr15:55511265..55513326,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000137876	Chromatin interaction
ENSG00000069974	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10518803	1.00[ASN][1000 genomes]
rs10518805	0.95[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	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12439213	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12439264	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12440497	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12440550	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12441258	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12441307	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12442180	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12442920	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12442937	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16976218	0.82[EUR][1000 genomes]
rs16976220	0.82[EUR][1000 genomes]
rs17238178	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17238220	0.82[EUR][1000 genomes]
rs17819000	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17819012	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28499877	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28705006	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs557254	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61638549	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7170936	1.00[ASN][1000 genomes]
rs7173803	1.00[ASN][1000 genomes]
rs7177930	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8039254	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9920531	0.95[EUR][1000 genomes];0.83[ASN][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	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

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:55489600-55513200	Weak transcription	Lung	lung
2	chr15:55489800-55540200	Weak transcription	Esophagus	oesophagus
3	chr15:55490000-55513000	Weak transcription	Fetal Intestine Large	intestine
4	chr15:55490000-55513200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr15:55490000-55513200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr15:55490000-55513200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr15:55490000-55517200	Weak transcription	Aorta	Aorta
8	chr15:55490000-55529400	Weak transcription	Rectal Smooth Muscle	rectum
9	chr15:55490000-55562800	Weak transcription	Ovary	ovary
10	chr15:55490200-55513200	Weak transcription	Duodenum Mucosa	Duodenum
11	chr15:55490200-55513800	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr15:55490200-55514000	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr15:55490400-55512600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr15:55491000-55513600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr15:55497800-55513000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr15:55497800-55513000	Weak transcription	Hela-S3	cervix
17	chr15:55497800-55514000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr15:55497800-55518400	Weak transcription	Gastric	stomach
19	chr15:55498000-55512800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr15:55498000-55512800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr15:55498000-55513200	Weak transcription	Primary T cells from cord blood	blood
22	chr15:55498000-55513400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr15:55498000-55514200	Weak transcription	Stomach Smooth Muscle	stomach
24	chr15:55506000-55514000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr15:55507000-55513000	Weak transcription	Fetal Intestine Small	intestine
26	chr15:55508400-55517000	Weak transcription	Fetal Heart	heart
27	chr15:55508600-55513200	Weak transcription	Thymus	Thymus
28	chr15:55508600-55522600	Weak transcription	Colon Smooth Muscle	Colon
29	chr15:55509000-55512600	Genic enhancers	Primary neutrophils fromperipheralblood	blood
30	chr15:55509000-55513000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr15:55509400-55541600	Weak transcription	Small Intestine	intestine
32	chr15:55510000-55512800	Enhancers	Primary B cells from cord blood	blood
33	chr15:55510200-55514600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr15:55510400-55512600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr15:55510400-55513000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr15:55510400-55517200	Weak transcription	Fetal Muscle Leg	muscle
37	chr15:55510400-55522600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr15:55510400-55525000	Weak transcription	Fetal Muscle Trunk	muscle
39	chr15:55510400-55528000	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr15:55510600-55512600	Weak transcription	NHLF	lung
41	chr15:55510600-55512800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr15:55510600-55512800	Weak transcription	HMEC	breast
43	chr15:55510600-55513000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr15:55510600-55513000	Weak transcription	Primary B cells from peripheral blood	blood
45	chr15:55510600-55513000	Weak transcription	Primary hematopoietic stem cells	blood
46	chr15:55510600-55513000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr15:55510600-55513000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr15:55510600-55513000	Weak transcription	HepG2	liver
49	chr15:55510600-55513200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr15:55510600-55513200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links