Variant report

Variant	rs12094028
Chromosome Location	chr1:45248869-45248870
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:45248830-45249152	K562	blood:	n/a	n/a
2	POLR2A	chr1:45248814-45249211	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr1:45240547-45249219	HepG2	liver:	n/a	n/a
4	POLR2A	chr1:45239529-45250168	SK-N-MC	brain:	n/a	n/a
5	POLR2A	chr1:45248743-45249147	ECC-1	luminal epithelium:	n/a	n/a
6	POLR2A	chr1:45248368-45249901	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr1:45248408-45250153	NB4	blood:	n/a	n/a
8	POLR2A	chr1:45248866-45249139	GM12878	blood:	n/a	n/a
9	POLR2A	chr1:45245085-45249976	PANC-1	pancreas:	n/a	n/a
10	POLR2A	chr1:45248831-45249189	GM12891	blood:	n/a	n/a
11	POLR2A	chr1:45248796-45249065	MCF-7	breast:	n/a	n/a
12	POLR2A	chr1:45248855-45249152	GM12878	blood:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:45246917..45250948-chr1:45965225..45967473,3	K562	blood:
2	chr1:45248852..45254229-chr1:45263166..45267959,10	MCF-7	breast:
3	chr1:45194298..45199848-chr1:45247467..45253056,11	MCF-7	breast:
4	chr1:45248846..45251148-chr1:46047782..46051549,3	K562	blood:
5	chr1:45238319..45262026-chr1:45262351..45301953,358	K562	blood:
6	chr1:45248546..45252735-chr1:45278815..45281288,3	MCF-7	breast:
7	chr1:45248577..45250762-chr1:45371713..45373726,2	K562	blood:
8	chr1:45246681..45259677-chr1:45281336..45290057,25	MCF-7	breast:
9	chr1:45248330..45252127-chr1:45262500..45268022,8	MCF-7	breast:
10	chr1:45248400..45253844-chr1:45268438..45273783,8	MCF-7	breast:
11	chr1:45248466..45253060-chr1:45282997..45288611,7	MCF-7	breast:

No data

Variant related genes	Relation type
RPS15AP11	TF binding region
ENSG00000202444	Chromatin interaction
ENSG00000188396	Chromatin interaction
ENSG00000132763	Chromatin interaction
ENSG00000173846	Chromatin interaction
ENSG00000132780	Chromatin interaction
ENSG00000200169	Chromatin interaction
ENSG00000117425	Chromatin interaction
ENSG00000222009	Chromatin interaction
ENSG00000236624	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10127448	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10465818	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11211030	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11211031	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11211034	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11584031	0.85[ASN][1000 genomes]
rs11801067	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11808189	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11808852	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12117881	0.84[ASN][1000 genomes]
rs12136048	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12136099	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12742914	0.81[ASN][1000 genomes]
rs16832228	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4542248	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6429548	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6656337	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6658470	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6666987	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6671255	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6678729	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6685176	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6688710	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6698847	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7512710	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7518836	0.85[ASN][1000 genomes]
rs7524446	0.86[EUR][1000 genomes]
rs7536146	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7550170	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7555065	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9988580	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533037	chr1:44361728-45333408	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
2	nsv998476	chr1:45001278-45311757	Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
3	nsv534941	chr1:45001278-45311757	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
4	nsv1014894	chr1:45139123-45397943	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	414 gene(s)	inside rSNPs	diseases
5	nsv529677	chr1:45179509-45748571	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers 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	424 gene(s)	inside rSNPs	diseases
6	nsv1002026	chr1:45187594-45758048	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	386 gene(s)	inside rSNPs	diseases
7	nsv998871	chr1:45196587-45251179	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	171 gene(s)	inside rSNPs	diseases
8	nsv461406	chr1:45218542-45293518	Strong transcription Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	127 gene(s)	inside rSNPs	diseases
9	nsv546145	chr1:45218542-45293518	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	127 gene(s)	inside rSNPs	diseases
10	nsv870815	chr1:45233638-45318752	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	127 gene(s)	inside rSNPs	diseases
11	nsv947252	chr1:45242176-45258816	Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45243400-45249000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr1:45243600-45249000	Strong transcription	Primary B cells from cord blood	blood
3	chr1:45243600-45249400	Weak transcription	Right Atrium	heart
4	chr1:45244000-45249000	Weak transcription	Fetal Lung	lung
5	chr1:45244000-45249800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr1:45244000-45249800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr1:45244200-45249000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr1:45244200-45249400	Weak transcription	Fetal Brain Male	brain
9	chr1:45244200-45249400	Strong transcription	Fetal Intestine Small	intestine
10	chr1:45244600-45249200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:45244600-45249400	Weak transcription	Psoas Muscle	Psoas
12	chr1:45244600-45251600	Weak transcription	Small Intestine	intestine
13	chr1:45244800-45249000	Weak transcription	Fetal Heart	heart
14	chr1:45244800-45249000	Weak transcription	NHDF-Ad	bronchial
15	chr1:45244800-45249200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr1:45244800-45249200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr1:45244800-45249400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:45244800-45249400	Weak transcription	Brain Cingulate Gyrus	brain
19	chr1:45244800-45249400	Weak transcription	Fetal Kidney	kidney
20	chr1:45244800-45249400	Weak transcription	Stomach Mucosa	stomach
21	chr1:45245000-45249000	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr1:45245000-45249400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr1:45245000-45249400	Weak transcription	Brain Substantia Nigra	brain
24	chr1:45245000-45249400	Weak transcription	NH-A	brain
25	chr1:45245000-45258600	Weak transcription	Hela-S3	cervix
26	chr1:45245200-45249200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr1:45245200-45249400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr1:45245200-45249400	Weak transcription	Gastric	stomach
29	chr1:45245600-45249000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr1:45245600-45249600	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr1:45245800-45249000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr1:45246000-45249400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr1:45246200-45249000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr1:45246200-45249000	Weak transcription	HepG2	liver
35	chr1:45246400-45249400	Weak transcription	Aorta	Aorta
36	chr1:45246400-45251400	Weak transcription	HSMMtube	muscle
37	chr1:45246600-45249000	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr1:45246600-45249200	Weak transcription	Brain Anterior Caudate	brain
39	chr1:45246600-45249400	Weak transcription	HMEC	breast
40	chr1:45246800-45249200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr1:45246800-45249200	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr1:45247000-45249200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr1:45247000-45249400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr1:45247000-45249400	Weak transcription	Stomach Smooth Muscle	stomach
45	chr1:45247000-45249400	Weak transcription	Osteobl	bone
46	chr1:45247200-45249000	Weak transcription	Lung	lung
47	chr1:45247200-45249200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr1:45247200-45249200	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr1:45247200-45249200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr1:45247200-45249200	Weak transcription	NHLF	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links