Variant report

Variant	rs2615239
Chromosome Location	chr15:57425493-57425494
allele	A/G
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	TCF12	chr15:57425195-57426138	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr15:57425438-57425962	H1-neurons	neurons:	n/a	n/a
3	MAX	chr15:57425489-57425873	ECC-1	luminal epithelium:	n/a	n/a
4	POLR2A	chr15:57425449-57425976	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:57411738..57417145-chr15:57421254..57425802,5	K562	blood:

Variant related genes	Relation type
TCF12	TF binding region

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1652733	1.00[YRI][hapmap]
rs2243575	1.00[AMR][1000 genomes]
rs2245616	1.00[YRI][hapmap]
rs2252366	1.00[YRI][hapmap]
rs2435899	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2435904	1.00[YRI][hapmap]
rs2439924	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2544128	1.00[YRI][hapmap]
rs2566847	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2585074	1.00[YRI][hapmap]
rs2585079	1.00[AMR][1000 genomes]
rs2585085	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2585095	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2585101	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2585109	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2585113	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2585122	1.00[YRI][hapmap]
rs2591073	1.00[YRI][hapmap]
rs2593245	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2593247	0.85[AFR][1000 genomes]
rs2593248	0.85[AFR][1000 genomes]
rs2593253	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs2615234	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2615245	0.85[AFR][1000 genomes]
rs2615247	1.00[AMR][1000 genomes]
rs2703581	1.00[AMR][1000 genomes]
rs2703585	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2703611	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2703617	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2703621	1.00[AMR][1000 genomes]
rs2733173	1.00[YRI][hapmap]
rs2733175	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2733184	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2733308	1.00[AMR][1000 genomes]
rs2733338	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042486	chr15:57094598-57505992	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv904251	chr15:57241970-57575916	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1045611	chr15:57350965-58070807	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57386400-57426600	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr15:57387000-57430000	Weak transcription	Placenta	Placenta
3	chr15:57387600-57442400	Weak transcription	Fetal Intestine Large	intestine
4	chr15:57406800-57425600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr15:57406800-57425600	Weak transcription	Fetal Muscle Trunk	muscle
6	chr15:57406800-57426400	Weak transcription	Colonic Mucosa	Colon
7	chr15:57406800-57426600	Weak transcription	Psoas Muscle	Psoas
8	chr15:57407600-57425600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr15:57410600-57426600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr15:57410600-57440800	Weak transcription	Ovary	ovary
11	chr15:57410800-57425600	Weak transcription	HMEC	breast
12	chr15:57411000-57428200	Weak transcription	NHLF	lung
13	chr15:57411000-57430400	Weak transcription	NH-A	brain
14	chr15:57411400-57426200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr15:57413800-57426600	Weak transcription	Duodenum Mucosa	Duodenum
16	chr15:57413800-57428800	Weak transcription	Gastric	stomach
17	chr15:57415000-57427800	Weak transcription	Colon Smooth Muscle	Colon
18	chr15:57415000-57428400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr15:57415000-57438800	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr15:57415200-57425600	Weak transcription	Aorta	Aorta
21	chr15:57415400-57426800	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr15:57415600-57438800	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr15:57416000-57438800	Weak transcription	Primary B cells from cord blood	blood
24	chr15:57416800-57425600	Weak transcription	Liver	Liver
25	chr15:57416800-57430800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr15:57417400-57426600	Weak transcription	Fetal Stomach	stomach
27	chr15:57417600-57426600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr15:57419000-57427000	Weak transcription	A549	lung
29	chr15:57419000-57428400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr15:57419600-57439000	Weak transcription	Fetal Intestine Small	intestine
31	chr15:57420600-57428200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr15:57421800-57425600	Weak transcription	Right Atrium	heart
33	chr15:57421800-57436600	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr15:57422200-57425600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr15:57422600-57425600	Weak transcription	Fetal Lung	lung
36	chr15:57422600-57430400	Weak transcription	Fetal Heart	heart
37	chr15:57423200-57428400	Enhancers	Primary T cells from cord blood	blood
38	chr15:57424200-57425800	Genic enhancers	Fetal Thymus	thymus
39	chr15:57424200-57428400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr15:57424400-57428600	Enhancers	HUES64 Cell Line	embryonic stem cell
41	chr15:57424600-57425600	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr15:57424600-57425800	Enhancers	Thymus	Thymus
43	chr15:57424600-57426800	Enhancers	HUVEC	blood vessel
44	chr15:57424600-57427400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr15:57424600-57428200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr15:57424600-57428200	Enhancers	Primary T helper cells PMA-I stimulated	--
47	chr15:57424600-57428400	Enhancers	iPS-18 Cell Line	embryonic stem cell
48	chr15:57424800-57425600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr15:57424800-57425600	Enhancers	Brain Cingulate Gyrus	brain
50	chr15:57424800-57425600	Enhancers	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links