Variant report

Variant	rs17238178
Chromosome Location	chr15:55507489-55507490
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:55506823..55512825-chr15:55581621..55584797,8	K562	blood:
2	chr15:55504661..55507549-chr15:55511770..55516084,4	K562	blood:
3	chr15:55506823..55513814-chr15:55580257..55584341,9	K562	blood:
4	chr15:55502637..55507829-chr15:55507957..55511534,4	MCF-7	breast:
5	chr15:55487591..55491418-chr15:55506365..55509165,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137876	Chromatin interaction
ENSG00000069974	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10518803	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10518805	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12324754	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12324775	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12438278	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12439213	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12439264	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12439890	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs12440497	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12440550	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12441258	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12441307	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12442180	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12442887	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12442920	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12442937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16976218	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs16976220	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs16976227	1.00[CEU][hapmap]
rs16976229	1.00[CEU][hapmap]
rs16976231	1.00[CEU][hapmap]
rs17238192	0.88[MEX][hapmap];0.82[AMR][1000 genomes]
rs17238199	0.82[AMR][1000 genomes]
rs17238206	0.82[AMR][1000 genomes]
rs17238220	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs17819000	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17819012	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17819024	0.82[AMR][1000 genomes]
rs17819036	0.83[AMR][1000 genomes]
rs28499877	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28705006	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs557254	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61638549	0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7170936	1.00[ASN][1000 genomes]
rs7171029	1.00[CEU][hapmap]
rs7171897	1.00[CEU][hapmap]
rs7173803	1.00[ASN][1000 genomes]
rs7177930	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8039254	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[TSI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9920531	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[TSI][hapmap];0.93[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:55 , 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	chr15:55490000-55509600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr15:55490000-55510000	Weak transcription	NHLF	lung
5	chr15:55490000-55513000	Weak transcription	Fetal Intestine Large	intestine
6	chr15:55490000-55513200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr15:55490000-55513200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr15:55490000-55513200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr15:55490000-55517200	Weak transcription	Aorta	Aorta
10	chr15:55490000-55529400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr15:55490000-55562800	Weak transcription	Ovary	ovary
12	chr15:55490200-55510000	Weak transcription	Fetal Kidney	kidney
13	chr15:55490200-55510200	Weak transcription	Fetal Lung	lung
14	chr15:55490200-55511400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr15:55490200-55511400	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr15:55490200-55511400	Weak transcription	Osteobl	bone
17	chr15:55490200-55513200	Weak transcription	Duodenum Mucosa	Duodenum
18	chr15:55490200-55513800	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr15:55490200-55514000	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr15:55490400-55510000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr15:55490400-55512600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr15:55490600-55510200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr15:55491000-55513600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr15:55497800-55510000	Weak transcription	Primary B cells from cord blood	blood
25	chr15:55497800-55511200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr15:55497800-55513000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr15:55497800-55513000	Weak transcription	Hela-S3	cervix
28	chr15:55497800-55514000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr15:55497800-55518400	Weak transcription	Gastric	stomach
30	chr15:55498000-55509400	Weak transcription	Stomach Mucosa	stomach
31	chr15:55498000-55509600	Weak transcription	Primary B cells from peripheral blood	blood
32	chr15:55498000-55509600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr15:55498000-55510000	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr15:55498000-55510000	Weak transcription	Liver	Liver
35	chr15:55498000-55510200	Weak transcription	Primary hematopoietic stem cells	blood
36	chr15:55498000-55510200	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr15:55498000-55510400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr15:55498000-55512800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr15:55498000-55512800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr15:55498000-55513200	Weak transcription	Primary T cells from cord blood	blood
41	chr15:55498000-55513400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr15:55498000-55514200	Weak transcription	Stomach Smooth Muscle	stomach
43	chr15:55498200-55509600	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr15:55498400-55512400	Weak transcription	Fetal Stomach	stomach
45	chr15:55499800-55510200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr15:55501200-55508000	Weak transcription	K562	blood
47	chr15:55502800-55509000	Strong transcription	Primary neutrophils fromperipheralblood	blood
48	chr15:55504200-55509000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr15:55504200-55509600	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr15:55506000-55510200	Weak transcription	Primary hematopoietic stem cells short term culture	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links