Variant report

Variant	rs1122890
Chromosome Location	chr15:57596048-57596049
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:6)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:57591325-57596303	NB4	blood:	n/a	n/a
2	POLR2A	chr15:57592667-57596467	HL-60	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TCF12-1	chr15:57595781-57596815	ENSG00000247982
2	lnc-TCF12-1	chr15:57595100-57599266	XLOC_011264
3	lnc-TCF12-1	chr15:57595100-57599967	XLOC_011264
4	lnc-TCF12-1	chr15:57595298-57599266	XLOC_011264
5	lnc-TCF12-1	chr15:57595100-57596248	XLOC_011264
6	lnc-TCF12-1	chr15:57595725-57596125	NONHSAT044059

No data

Variant related genes	Relation type
LINC00926	TF binding region

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

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10518910	1.00[CEU][hapmap]
rs12438324	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12438331	1.00[AFR][1000 genomes]
rs12438428	1.00[CEU][hapmap]
rs12438782	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs12438954	1.00[AFR][1000 genomes]
rs12439374	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12440699	1.00[CEU][hapmap]
rs12440878	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs12441107	1.00[AFR][1000 genomes]
rs12442879	1.00[CEU][hapmap]
rs12443006	0.80[EUR][1000 genomes]
rs12443076	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs12443097	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs1462157	1.00[CEU][hapmap]
rs17239522	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs17239543	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17819994	1.00[CEU][hapmap]
rs17820077	1.00[AFR][1000 genomes]
rs17820119	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs17820131	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs2126398	1.00[CEU][hapmap]
rs2414499	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2591050	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4514619	1.00[CEU][hapmap]
rs8024992	0.82[AMR][1000 genomes]
rs8031866	1.00[CEU][hapmap]

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	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
2	nsv833021	chr15:57495413-57751366	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv526342	chr15:57565859-57597280	Strong transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57537800-57598200	Weak transcription	Colonic Mucosa	Colon
2	chr15:57578600-57598200	Weak transcription	Right Ventricle	heart
3	chr15:57579600-57598200	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr15:57580000-57598400	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr15:57580000-57598400	Weak transcription	Fetal Brain Male	brain
6	chr15:57580000-57598400	Weak transcription	NHEK	skin
7	chr15:57583400-57598400	Weak transcription	Thymus	Thymus
8	chr15:57583600-57598000	Weak transcription	Liver	Liver
9	chr15:57583600-57598200	Weak transcription	Stomach Smooth Muscle	stomach
10	chr15:57583600-57598400	Weak transcription	A549	lung
11	chr15:57583800-57596800	Weak transcription	Fetal Intestine Large	intestine
12	chr15:57584000-57598200	Weak transcription	Brain Germinal Matrix	brain
13	chr15:57584400-57598000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr15:57584400-57598200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr15:57584600-57598200	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr15:57584600-57598200	Weak transcription	Fetal Stomach	stomach
17	chr15:57585000-57598400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr15:57585600-57598000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr15:57585800-57598200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr15:57589200-57598200	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr15:57589400-57598200	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr15:57589400-57598200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr15:57589600-57598200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr15:57589600-57598400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr15:57590000-57597000	Weak transcription	Fetal Intestine Small	intestine
26	chr15:57590000-57598200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr15:57590000-57598200	Weak transcription	Pancreas	Pancrea
28	chr15:57590800-57598200	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr15:57591000-57598000	Weak transcription	Brain Anterior Caudate	brain
30	chr15:57591600-57598200	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr15:57591800-57596800	Weak transcription	Duodenum Mucosa	Duodenum
32	chr15:57591800-57598000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr15:57592000-57598000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr15:57592000-57598400	Weak transcription	HSMMtube	muscle
35	chr15:57592200-57597400	Weak transcription	Fetal Muscle Leg	muscle
36	chr15:57592200-57598200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr15:57592200-57598400	Weak transcription	HMEC	breast
38	chr15:57592200-57598400	Weak transcription	NHLF	lung
39	chr15:57592400-57598000	Weak transcription	Fetal Lung	lung
40	chr15:57592400-57598000	Weak transcription	Fetal Muscle Trunk	muscle
41	chr15:57592400-57598200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr15:57592400-57598200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr15:57592400-57598400	Weak transcription	Placenta	Placenta
44	chr15:57592600-57598200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr15:57592600-57598200	Weak transcription	Spleen	Spleen
46	chr15:57593000-57598200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr15:57593800-57599200	Weak transcription	Small Intestine	intestine
48	chr15:57593800-57599400	Transcr. at gene 5' and 3'	Primary B cells from peripheral blood	blood
49	chr15:57594000-57598200	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr15:57595000-57598200	Weak transcription	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links