Variant report

Variant	rs4768048
Chromosome Location	chr12:44228872-44228873
allele	C/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	chr12:44228793-44230771	Raji	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:44151301..44154228-chr12:44227613..44229712,2	K562	blood:
2	chr12:44198221..44201924-chr12:44226822..44231143,11	MCF-7	breast:
3	chr12:44197117..44201952-chr12:44227919..44231382,13	MCF-7	breast:

Variant related genes	Relation type
TMEM117	TF binding region
ENSG00000151239	Chromatin interaction
ENSG00000129317	Chromatin interaction
ENSG00000198001	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs12370425	1.00[JPT][hapmap]
rs4768537	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7962590	0.82[ASN][1000 genomes]
rs7969372	1.00[CHB][hapmap];1.00[JPT][hapmap]

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	nsv933142	chr12:44130156-44278300	Active TSS Flanking Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv899048	chr12:44209423-44307888	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4768048	PPHLN1	cis	parietal	SCAN

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:44223400-44229000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr12:44223400-44229000	Weak transcription	Osteobl	bone
3	chr12:44223800-44229000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr12:44223800-44229000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr12:44224000-44229000	Weak transcription	NHEK	skin
6	chr12:44224200-44229000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr12:44224200-44229200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr12:44225000-44229200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr12:44226200-44229000	Weak transcription	Small Intestine	intestine
10	chr12:44227000-44229000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr12:44227000-44229000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr12:44227800-44229200	Weak transcription	Lung	lung
13	chr12:44227800-44231800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr12:44228200-44229200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr12:44228600-44229000	Enhancers	Primary T cells from cord blood	blood
16	chr12:44228600-44229000	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr12:44228600-44229000	Enhancers	Adipose Nuclei	Adipose
18	chr12:44228600-44229000	Enhancers	Brain Anterior Caudate	brain
19	chr12:44228600-44229000	Enhancers	Brain Inferior Temporal Lobe	brain
20	chr12:44228600-44229000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
21	chr12:44228600-44229000	Enhancers	Fetal Brain Male	brain
22	chr12:44228600-44229000	Enhancers	Hela-S3	cervix
23	chr12:44228600-44229200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr12:44228600-44229200	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr12:44228600-44229200	Enhancers	Placenta	Placenta
26	chr12:44228600-44229200	Enhancers	Thymus	Thymus
27	chr12:44228600-44229400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr12:44228600-44229400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr12:44228600-44230800	Active TSS	Psoas Muscle	Psoas
30	chr12:44228800-44229000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr12:44228800-44229000	Bivalent/Poised TSS	Primary B cells from cord blood	blood
32	chr12:44228800-44229000	Active TSS	Primary T cells fromperipheralblood	blood
33	chr12:44228800-44229000	Active TSS	Primary hematopoietic stem cells	blood
34	chr12:44228800-44229000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr12:44228800-44229000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr12:44228800-44229000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr12:44228800-44229000	Enhancers	Brain Angular Gyrus	brain
38	chr12:44228800-44229000	Enhancers	Brain Cingulate Gyrus	brain
39	chr12:44228800-44229000	Enhancers	Brain Substantia Nigra	brain
40	chr12:44228800-44229000	Flanking Active TSS	Colon Smooth Muscle	Colon
41	chr12:44228800-44229000	Enhancers	Duodenum Mucosa	Duodenum
42	chr12:44228800-44229000	Enhancers	Fetal Heart	heart
43	chr12:44228800-44229000	Enhancers	Fetal Intestine Small	intestine
44	chr12:44228800-44229000	Enhancers	Fetal Kidney	kidney
45	chr12:44228800-44229000	Enhancers	Fetal Muscle Leg	muscle
46	chr12:44228800-44229000	Enhancers	Pancreas	Pancrea
47	chr12:44228800-44229000	Enhancers	Stomach Smooth Muscle	stomach
48	chr12:44228800-44229000	Enhancers	A549	lung
49	chr12:44228800-44229000	Active TSS	HepG2	liver
50	chr12:44228800-44229000	Enhancers	NHDF-Ad	bronchial

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