Variant report

Variant	rs1862044
Chromosome Location	chr12:50576146-50576147
allele	A/C
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	RAD21	chr12:50576142-50576755	MCF-7	breast:	n/a	chr12:50576426-50576445
2	CTCF	chr12:50576132-50576689	HCT-116	colon:	n/a	chr12:50576427-50576448 chr12:50576425-50576443
3	RAD21	chr12:50576090-50576747	MCF-7	breast:	n/a	chr12:50576426-50576445
4	CTCF	chr12:50576099-50576784	A549	lung:	n/a	chr12:50576427-50576448 chr12:50576425-50576443
5	RAD21	chr12:50576123-50576814	HCT-116	colon:	n/a	chr12:50576426-50576445
6	RAD21	chr12:50576133-50576761	A549	lung:	n/a	chr12:50576426-50576445

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:50575985..50576844-chr12:50708187..50709140,4	K562	blood:

Variant related genes	Relation type
LIMA1	TF binding region

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10450773	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10783336	0.89[CHB][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap]
rs10783337	0.89[CHB][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap]
rs10783341	0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10876006	0.89[CHB][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap]
rs10876007	0.94[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs10876011	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11169283	0.88[CHB][hapmap];0.89[JPT][hapmap]
rs11169284	0.87[CHB][hapmap];0.89[JPT][hapmap]
rs11169312	0.90[ASN][1000 genomes]
rs17124448	0.89[CHB][hapmap];0.85[JPT][hapmap]
rs2242507	0.89[CHB][hapmap];0.85[JPT][hapmap]
rs2277355	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs7297864	0.81[ASN][1000 genomes]
rs7300549	0.80[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[ASN][1000 genomes]
rs73106145	0.83[ASN][1000 genomes]
rs73106156	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7314598	0.89[CHB][hapmap];0.85[JPT][hapmap]
rs7397849	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	esv3392138	chr12:50394642-50645326	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1862044	LASS5	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50561800-50582600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr12:50561800-50582600	Weak transcription	Stomach Mucosa	stomach
3	chr12:50562000-50576400	Weak transcription	A549	lung
4	chr12:50562000-50584800	Weak transcription	K562	blood
5	chr12:50562200-50597000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr12:50564400-50586200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr12:50564400-50600800	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr12:50567800-50578800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr12:50568200-50578200	Strong transcription	Fetal Intestine Large	intestine
10	chr12:50568600-50577800	Strong transcription	NHDF-Ad	bronchial
11	chr12:50568600-50582000	Weak transcription	Primary B cells from peripheral blood	blood
12	chr12:50568800-50581400	Strong transcription	Fetal Muscle Trunk	muscle
13	chr12:50569200-50577000	Strong transcription	Osteobl	bone
14	chr12:50569200-50579000	Strong transcription	NHEK	skin
15	chr12:50569400-50577800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr12:50569400-50579000	Weak transcription	Fetal Brain Male	brain
17	chr12:50569400-50581400	Weak transcription	Brain Substantia Nigra	brain
18	chr12:50569600-50579400	Strong transcription	Duodenum Mucosa	Duodenum
19	chr12:50569800-50576400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr12:50569800-50577000	Strong transcription	Adipose Nuclei	Adipose
21	chr12:50569800-50577400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr12:50569800-50577800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr12:50569800-50578200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr12:50569800-50578200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr12:50569800-50578800	Strong transcription	Fetal Muscle Leg	muscle
26	chr12:50570000-50576200	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr12:50570000-50577400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr12:50570000-50578000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr12:50570000-50601400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr12:50570400-50592800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr12:50570600-50582800	Weak transcription	Small Intestine	intestine
32	chr12:50570800-50579800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr12:50570800-50580000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr12:50570800-50589800	Strong transcription	Fetal Stomach	stomach
35	chr12:50571200-50579000	Strong transcription	Fetal Intestine Small	intestine
36	chr12:50571600-50581400	Weak transcription	Rectal Smooth Muscle	rectum
37	chr12:50571800-50579000	Weak transcription	Aorta	Aorta
38	chr12:50571800-50579000	Weak transcription	Pancreas	Pancrea
39	chr12:50571800-50579200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr12:50571800-50579800	Weak transcription	Gastric	stomach
41	chr12:50571800-50579800	Weak transcription	Psoas Muscle	Psoas
42	chr12:50571800-50580200	Weak transcription	HepG2	liver
43	chr12:50571800-50581400	Weak transcription	Spleen	Spleen
44	chr12:50571800-50586000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr12:50571800-50586200	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr12:50571800-50595800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr12:50571800-50597000	Weak transcription	Thymus	Thymus
48	chr12:50571800-50597600	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr12:50571800-50614200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr12:50572000-50579200	Weak transcription	Brain Cingulate Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links