Variant report

Variant	rs4742815
Chromosome Location	chr9:104230806-104230807
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	ELF1	chr9:104230431-104230806	K562	blood:	n/a	chr9:104230642-104230655
2	USF1	chr9:104230388-104230859	HCT-116	colon:	n/a	n/a
3	USF1	chr9:104230385-104230813	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:104230694..104236463-chr9:104246967..104249431,5	K562	blood:
2	chr9:104197118..104199793-chr9:104230175..104232444,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RNF20-1	chr9:104230744-104230890	ENSG00000225376.1

Variant related genes	Relation type
ENSG00000225376	TF binding region
ENSG00000136872	Chromatin interaction
ENSG00000165152	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10819945	0.87[ASN][1000 genomes]
rs10989528	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10989529	0.92[ASN][1000 genomes]
rs16920420	0.93[ASN][1000 genomes]
rs57815349	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046975	chr9:104167583-104659873	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv893626	chr9:104172936-104324545	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv614962	chr9:104204614-104240708	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv949579	chr9:104229820-104512923	Genic enhancers Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4742815	TMEM246	cis	Nerve Tibial	GTEx
rs4742815	RP11-490D19.6	cis	Nerve Tibial	GTEx

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:104212000-104241400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr9:104221800-104235000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr9:104222000-104236400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr9:104224800-104235000	Weak transcription	Pancreas	Pancrea
5	chr9:104225000-104237800	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr9:104225400-104235800	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr9:104225400-104237200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr9:104226000-104239200	Weak transcription	NH-A	brain
9	chr9:104226400-104236400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr9:104226600-104235200	Weak transcription	Ovary	ovary
11	chr9:104226600-104236200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr9:104226600-104238200	Weak transcription	Esophagus	oesophagus
13	chr9:104227200-104231800	Weak transcription	Right Ventricle	heart
14	chr9:104227600-104235600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr9:104227800-104232200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr9:104227800-104234200	Weak transcription	Duodenum Mucosa	Duodenum
17	chr9:104227800-104235000	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr9:104227800-104235200	Weak transcription	Fetal Intestine Large	intestine
19	chr9:104227800-104235800	Weak transcription	Aorta	Aorta
20	chr9:104227800-104238200	Weak transcription	Colonic Mucosa	Colon
21	chr9:104227800-104242800	Weak transcription	K562	blood
22	chr9:104227800-104248200	Weak transcription	Liver	Liver
23	chr9:104228000-104235800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr9:104228000-104236600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr9:104228000-104238000	Weak transcription	A549	lung
26	chr9:104228000-104240000	Weak transcription	Colon Smooth Muscle	Colon
27	chr9:104228200-104235800	Weak transcription	Adipose Nuclei	Adipose
28	chr9:104228200-104237600	Weak transcription	Fetal Intestine Small	intestine
29	chr9:104228400-104234600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr9:104228400-104237800	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr9:104228400-104239200	Weak transcription	Hela-S3	cervix
32	chr9:104228400-104240400	Weak transcription	Fetal Heart	heart
33	chr9:104229000-104235400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr9:104229000-104239200	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr9:104229000-104239600	Weak transcription	NHEK	skin
36	chr9:104229000-104240000	Weak transcription	NHDF-Ad	bronchial
37	chr9:104229000-104248200	Weak transcription	NHLF	lung
38	chr9:104229200-104235800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr9:104229400-104231000	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr9:104229400-104231000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr9:104229600-104234200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr9:104229600-104236600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr9:104229800-104231000	Enhancers	Stomach Mucosa	stomach
44	chr9:104230200-104231200	Enhancers	iPS-18 Cell Line	embryonic stem cell
45	chr9:104230200-104234400	Weak transcription	Fetal Brain Female	brain
46	chr9:104230200-104238000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr9:104230400-104231000	Enhancers	ES-I3 Cell Line	embryonic stem cell
48	chr9:104230400-104231000	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr9:104230400-104231200	Active TSS	Brain Hippocampus Middle	brain
50	chr9:104230400-104231200	Active TSS	Brain Inferior Temporal Lobe	brain

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