Variant report

Variant	rs56357916
Chromosome Location	chr17:38348616-38348617
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:38348399..38350901-chr17:38351389..38353492,2	MCF-7	breast:
2	chr17:38348080..38350590-chr17:38501950..38504205,2	K562	blood:
3	chr17:38330070..38334400-chr17:38346938..38351108,4	K562	blood:
4	chr17:38343298..38345399-chr17:38347624..38349920,2	MCF-7	breast:
5	chr17:38334977..38338913-chr17:38347829..38351366,4	MCF-7	breast:
6	chr17:38337616..38339944-chr17:38348078..38350196,2	K562	blood:
7	chr17:38268818..38270189-chr17:38347742..38348733,4	K562	blood:

Variant related genes	Relation type
ENSG00000108352	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs28786708	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34394173	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35085163	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs45443194	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55673000	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56304903	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7221536	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73306870	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833444	chr17:38242823-38437280	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv525796	chr17:38306365-38405037	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv3413265	chr17:38346576-38348974	Active TSS Genic enhancers Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs56357916	MSL1	cis	Esophagus Muscularis	GTEx
rs56357916	MSL1	cis	Thyroid	GTEx
rs56357916	MSL1	cis	Nerve Tibial	GTEx

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38338000-38349800	Weak transcription	Dnd41	blood
2	chr17:38347800-38348800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr17:38348000-38348800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
4	chr17:38348000-38350200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr17:38348000-38350400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr17:38348000-38350400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr17:38348000-38350400	Weak transcription	Gastric	stomach
8	chr17:38348000-38350800	Strong transcription	Sigmoid Colon	Sigmoid Colon
9	chr17:38348000-38351000	Weak transcription	Spleen	Spleen
10	chr17:38348000-38353400	Weak transcription	Aorta	Aorta
11	chr17:38348200-38348800	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr17:38348200-38348800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr17:38348200-38348800	Enhancers	Primary B cells from peripheral blood	blood
14	chr17:38348200-38348800	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr17:38348200-38348800	Weak transcription	Rectal Smooth Muscle	rectum
16	chr17:38348200-38349000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr17:38348200-38349000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr17:38348200-38349000	Enhancers	Fetal Thymus	thymus
19	chr17:38348200-38349800	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr17:38348200-38350000	Weak transcription	Lung	lung
21	chr17:38348200-38350200	Strong transcription	Colonic Mucosa	Colon
22	chr17:38348200-38350200	Strong transcription	Duodenum Mucosa	Duodenum
23	chr17:38348200-38350200	Weak transcription	HSMMtube	muscle
24	chr17:38348200-38350600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr17:38348200-38350800	Strong transcription	Rectal Mucosa Donor 31	rectum
26	chr17:38348200-38351600	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr17:38348200-38351600	Weak transcription	Right Ventricle	heart
28	chr17:38348200-38353200	Weak transcription	Thymus	Thymus
29	chr17:38348400-38348800	Enhancers	H1 Cell Line	embryonic stem cell
30	chr17:38348400-38348800	Enhancers	HUES48 Cell Line	embryonic stem cell
31	chr17:38348400-38348800	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr17:38348400-38348800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr17:38348400-38348800	Weak transcription	Fetal Brain Female	brain
34	chr17:38348400-38348800	Weak transcription	Placenta	Placenta
35	chr17:38348400-38348800	Weak transcription	Fetal Stomach	stomach
36	chr17:38348400-38348800	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr17:38348400-38348800	Enhancers	A549	lung
38	chr17:38348400-38348800	Enhancers	GM12878-XiMat	blood
39	chr17:38348400-38349000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr17:38348400-38349200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr17:38348400-38349200	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr17:38348400-38349200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr17:38348400-38349200	Weak transcription	Brain Angular Gyrus	brain
44	chr17:38348400-38349200	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr17:38348400-38349200	Weak transcription	Left Ventricle	heart
46	chr17:38348400-38349400	Weak transcription	Brain Anterior Caudate	brain
47	chr17:38348400-38349800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr17:38348400-38349800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr17:38348400-38349800	Weak transcription	Fetal Muscle Trunk	muscle
50	chr17:38348400-38349800	Strong transcription	NHEK	skin

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