Variant report

Variant	rs59990555
Chromosome Location	chr12:49726326-49726327
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:49725372..49727025-chr12:49731927..49734033,2	MCF-7	breast:
2	chr12:49690361..49691961-chr12:49725710..49727427,2	MCF-7	breast:
3	chr12:49724830..49727128-chr12:49748718..49750720,2	MCF-7	breast:
4	chr12:49680691..49694205-chr12:49725987..49738512,25	K562	blood:
5	chr12:49725096..49726573-chr12:49750546..49751554,11	MCF-7	breast:
6	chr12:49726070..49728754-chr12:49729345..49731828,3	MCF-7	breast:
7	chr12:49725094..49726383-chr12:49741023..49741965,3	MCF-7	breast:
8	chr12:49724052..49726858-chr12:49947435..49949990,2	K562	blood:
9	chr12:49725445..49728074-chr12:49906723..49908928,2	MCF-7	breast:
10	chr12:49724272..49727239-chr12:49903612..49905113,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000123352	Chromatin interaction
ENSG00000186897	Chromatin interaction
ENSG00000135406	Chromatin interaction
ENSG00000135519	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10875946	0.83[EUR][1000 genomes]
rs10875948	0.83[EUR][1000 genomes]
rs11168972	0.83[EUR][1000 genomes]
rs12318618	0.84[EUR][1000 genomes]
rs56911877	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57755392	0.81[EUR][1000 genomes]
rs61649357	0.95[EUR][1000 genomes]
rs73309973	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7397166	0.95[EUR][1000 genomes]
rs7398252	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
2	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases
4	nsv428801	chr12:49536659-49744884	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
5	nsv1042122	chr12:49678529-49823168	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
6	nsv1039176	chr12:49678529-49832618	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
7	nsv899068	chr12:49714103-49924637	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
8	nsv832405	chr12:49720279-49910862	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
9	nsv826368	chr12:49726310-49731802	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs59990555	C1QL4	cis	Thyroid	GTEx

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49717400-49726800	Weak transcription	Right Atrium	heart
2	chr12:49717800-49727000	Weak transcription	Esophagus	oesophagus
3	chr12:49718000-49726400	Weak transcription	Primary B cells from cord blood	blood
4	chr12:49718000-49730200	Weak transcription	Gastric	stomach
5	chr12:49721400-49727000	Weak transcription	NHDF-Ad	bronchial
6	chr12:49721600-49729600	Weak transcription	HSMM	muscle
7	chr12:49721800-49726400	Weak transcription	HUVEC	blood vessel
8	chr12:49724400-49727000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
9	chr12:49724600-49726400	Genic enhancers	A549	lung
10	chr12:49724600-49727000	Bivalent Enhancer	Fetal Stomach	stomach
11	chr12:49724600-49727000	Weak transcription	Osteobl	bone
12	chr12:49724600-49728800	Weak transcription	GM12878-XiMat	blood
13	chr12:49724800-49726600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr12:49725000-49726800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr12:49725000-49726800	Bivalent Enhancer	Fetal Muscle Leg	muscle
16	chr12:49725000-49727000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:49725000-49727000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr12:49725000-49727000	Enhancers	Placenta Amnion	Placenta Amnion
19	chr12:49725000-49728600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr12:49725000-49728600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr12:49725200-49726400	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr12:49725200-49726800	Weak transcription	HMEC	breast
23	chr12:49725400-49726400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr12:49725400-49726400	Weak transcription	NHEK	skin
25	chr12:49725400-49726600	Enhancers	Placenta	Placenta
26	chr12:49725400-49727000	Weak transcription	NHLF	lung
27	chr12:49725400-49728600	Weak transcription	HSMMtube	muscle
28	chr12:49725400-49730400	Weak transcription	Dnd41	blood
29	chr12:49725600-49726400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr12:49725600-49726800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr12:49725600-49727000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
32	chr12:49725600-49728000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr12:49725800-49726400	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr12:49725800-49726600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
35	chr12:49725800-49726600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr12:49725800-49730400	Weak transcription	Hela-S3	cervix
37	chr12:49726000-49726400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr12:49726000-49726600	Bivalent Enhancer	Brain Germinal Matrix	brain
39	chr12:49726000-49726800	Weak transcription	Liver	Liver
40	chr12:49726000-49727000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
41	chr12:49726000-49727400	Bivalent Enhancer	Fetal Intestine Large	intestine
42	chr12:49726200-49726400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
43	chr12:49726200-49726400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
44	chr12:49726200-49726400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr12:49726200-49726600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr12:49726200-49727400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell

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