Variant report

Variant	rs28442130
Chromosome Location	chr15:57593140-57593141
allele	G/T
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	POLR2A	chr15:57591325-57596303	NB4	blood:	n/a	n/a
2	RELA	chr15:57591673-57593287	GM19193	blood:	n/a	chr15:57592123-57592132 chr15:57592123-57592132
3	CHD1	chr15:57592975-57593345	GM12878	blood:	n/a	n/a
4	POLR2A	chr15:57591446-57594099	GM12891	blood:	n/a	n/a
5	MXI1	chr15:57593127-57593371	GM12878	blood:	n/a	n/a
6	WRNIP1	chr15:57592871-57594067	GM12878	blood:	n/a	n/a
7	BHLHE40	chr15:57591928-57593506	GM12878	blood:	n/a	n/a
8	RUNX3	chr15:57592848-57593497	GM12878	blood:	n/a	n/a
9	ZNF384	chr15:57593084-57593624	GM12878	blood:	n/a	n/a
10	POLR2A	chr15:57591163-57594122	GM12878	blood:	n/a	n/a
11	POLR2A	chr15:57592686-57593209	HL-60	blood:	n/a	n/a
12	POLR2A	chr15:57592667-57596467	HL-60	blood:	n/a	n/a
13	POLR2A	chr15:57591597-57593159	Raji	blood:	n/a	n/a
14	REST	chr15:57592723-57593217	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:57588417..57590307-chr15:57592744..57595404,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TCF12-1	chr15:57592198-57595211	XLOC_011264

Variant related genes	Relation type
LINC00926	TF binding region

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs16977281	1.00[AMR][1000 genomes]
rs16977359	1.00[AMR][1000 genomes]
rs16977360	1.00[AMR][1000 genomes]
rs74016154	1.00[AMR][1000 genomes]
rs8035840	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	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:72 , 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	chr15:57579800-57595000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr15:57580000-57598400	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr15:57580000-57598400	Weak transcription	Fetal Brain Male	brain
7	chr15:57580000-57598400	Weak transcription	NHEK	skin
8	chr15:57580600-57594800	Weak transcription	HepG2	liver
9	chr15:57581600-57595000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr15:57583400-57595000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr15:57583400-57598400	Weak transcription	Thymus	Thymus
12	chr15:57583600-57598000	Weak transcription	Liver	Liver
13	chr15:57583600-57598200	Weak transcription	Stomach Smooth Muscle	stomach
14	chr15:57583600-57598400	Weak transcription	A549	lung
15	chr15:57583800-57595400	Weak transcription	Aorta	Aorta
16	chr15:57583800-57596800	Weak transcription	Fetal Intestine Large	intestine
17	chr15:57584000-57598200	Weak transcription	Brain Germinal Matrix	brain
18	chr15:57584400-57598000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr15:57584400-57598200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr15:57584600-57594600	Weak transcription	Primary T cells from cord blood	blood
21	chr15:57584600-57598200	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr15:57584600-57598200	Weak transcription	Fetal Stomach	stomach
23	chr15:57585000-57598400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr15:57585600-57598000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr15:57585800-57598200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr15:57589200-57598200	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr15:57589400-57594800	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr15:57589400-57595000	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr15:57589400-57598200	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr15:57589400-57598200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr15:57589600-57595200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr15:57589600-57598200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr15:57589600-57598400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr15:57590000-57597000	Weak transcription	Fetal Intestine Small	intestine
35	chr15:57590000-57598200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr15:57590000-57598200	Weak transcription	Pancreas	Pancrea
37	chr15:57590400-57593600	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr15:57590800-57598200	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr15:57591000-57598000	Weak transcription	Brain Anterior Caudate	brain
40	chr15:57591600-57595400	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr15:57591600-57598200	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr15:57591800-57596800	Weak transcription	Duodenum Mucosa	Duodenum
43	chr15:57591800-57598000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr15:57592000-57598000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr15:57592000-57598400	Weak transcription	HSMMtube	muscle
46	chr15:57592200-57597400	Weak transcription	Fetal Muscle Leg	muscle
47	chr15:57592200-57598200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr15:57592200-57598400	Weak transcription	HMEC	breast
49	chr15:57592200-57598400	Weak transcription	NHLF	lung
50	chr15:57592400-57593400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links