Variant report

Variant	rs12126557
Chromosome Location	chr1:45257201-45257202
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr1:45257138-45257506	K562	blood:	n/a	n/a
2	MAZ	chr1:45257192-45257494	K562	blood:	n/a	n/a
3	ZBTB7A	chr1:45257199-45257522	K562	blood:	n/a	n/a
4	NFYB	chr1:45257140-45257490	K562	blood:	n/a	n/a
5	NR2F2	chr1:45257085-45257538	K562	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:45185596..45187362-chr1:45255952..45259330,3	MCF-7	breast:
2	chr1:45255472..45258874-chr1:45274413..45277511,4	MCF-7	breast:
3	chr1:45238319..45262026-chr1:45262351..45301953,358	K562	blood:
4	chr1:45256108..45258642-chr1:45958911..45960479,2	K562	blood:
5	chr1:45246681..45259677-chr1:45281336..45290057,25	MCF-7	breast:
6	chr1:45257179..45260410-chr1:45476355..45479438,4	K562	blood:
7	chr1:45257179..45261874-chr1:45476446..45479576,6	K562	blood:
8	chr1:45187577..45189400-chr1:45255993..45258974,2	MCF-7	breast:
9	chr1:45256101..45258337-chr1:45265559..45267061,2	MCF-7	breast:

No data

Variant related genes	Relation type
BEST4	TF binding region
ENSG00000126088	Chromatin interaction
ENSG00000188396	Chromatin interaction
ENSG00000117425	Chromatin interaction
ENSG00000126107	Chromatin interaction
ENSG00000173846	Chromatin interaction
ENSG00000222009	Chromatin interaction
ENSG00000202444	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11211024	0.91[CEU][hapmap]
rs11211036	0.85[CEU][hapmap]
rs11211038	0.84[CEU][hapmap]
rs11211040	0.84[CEU][hapmap]
rs11573562	0.84[CEU][hapmap]
rs11584440	0.84[CEU][hapmap]
rs11803622	0.84[CEU][hapmap]
rs12120833	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12127328	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12139143	0.84[CEU][hapmap]
rs12732939	0.85[CEU][hapmap]
rs12733586	0.92[CEU][hapmap]
rs12746270	0.84[CEU][hapmap]
rs16832210	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16832227	0.84[CEU][hapmap]
rs16832263	0.84[CEU][hapmap]
rs17881698	0.84[CEU][hapmap]
rs17883049	0.84[CEU][hapmap]
rs2295997	0.84[CEU][hapmap]
rs3795714	0.85[CEU][hapmap]
rs3795719	0.84[CEU][hapmap]
rs3820586	0.84[CEU][hapmap]
rs4342887	0.84[CEU][hapmap]
rs6429550	0.92[CEU][hapmap]
rs6676749	0.84[CEU][hapmap]
rs6689911	0.84[CEU][hapmap]
rs6692487	0.85[CEU][hapmap]
rs6703452	0.84[CEU][hapmap]
rs7517439	0.85[CEU][hapmap]
rs7517639	0.85[CEU][hapmap]
rs7534487	0.85[CEU][hapmap]
rs7546285	0.92[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
8	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
9	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
10	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12126557	UROD	cis	lung	GTEx

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45245000-45258600	Weak transcription	Hela-S3	cervix
2	chr1:45252400-45264200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr1:45252400-45265200	Weak transcription	Right Atrium	heart
4	chr1:45252400-45265600	Weak transcription	Gastric	stomach
5	chr1:45252600-45258800	Weak transcription	Esophagus	oesophagus
6	chr1:45252600-45258800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr1:45252600-45259000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr1:45252600-45262200	Weak transcription	Placenta	Placenta
9	chr1:45252600-45264200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:45252800-45258800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:45252800-45258800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr1:45252800-45259000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr1:45255400-45259600	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr1:45255400-45259800	Enhancers	K562	blood
15	chr1:45255600-45257400	Enhancers	Fetal Stomach	stomach
16	chr1:45255800-45258800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr1:45255800-45259000	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr1:45256000-45258600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr1:45256000-45258600	Weak transcription	HMEC	breast
20	chr1:45256000-45258800	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr1:45256000-45258800	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr1:45256000-45258800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr1:45256000-45264200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr1:45256000-45264800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:45256000-45265200	Weak transcription	NHEK	skin
26	chr1:45256600-45257400	Enhancers	Fetal Muscle Leg	muscle
27	chr1:45256800-45257400	Flanking Bivalent TSS/Enh	HepG2	liver
28	chr1:45256800-45257600	Enhancers	Pancreas	Pancrea
29	chr1:45256800-45257600	Enhancers	Rectal Mucosa Donor 31	rectum
30	chr1:45256800-45257600	Enhancers	Stomach Mucosa	stomach
31	chr1:45256800-45259200	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr1:45257000-45257400	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr1:45257000-45257400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr1:45257000-45257400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr1:45257000-45257400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr1:45257000-45257400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
37	chr1:45257000-45257600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr1:45257000-45257600	Enhancers	Fetal Intestine Large	intestine
39	chr1:45257200-45257400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr1:45257200-45257400	Enhancers	Duodenum Mucosa	Duodenum
41	chr1:45257200-45257600	Enhancers	Fetal Intestine Small	intestine
42	chr1:45257200-45258800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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