Variant report

Variant	rs2325750
Chromosome Location	chr17:46022330-46022331
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	chr17:46020199-46023291	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr17:46022329-46022346	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:45968434..45977260-chr17:46017847..46029594,27	MCF-7	breast:
2	chr17:46021116..46023804-chr17:46125669..46127456,2	K562	blood:

Variant related genes	Relation type
ENSG00000263798	TF binding region
ENSG00000234494	TF binding region
PNPO	TF binding region
ENSG00000082641	Chromatin interaction
ENSG00000167182	Chromatin interaction
ENSG00000264920	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1133221	0.87[CHB][hapmap];0.93[CHD][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs16949270	0.87[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs16949296	0.87[CHB][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs16949427	0.87[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs16949651	0.87[CHB][hapmap];0.80[CHD][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs17616799	0.81[CHB][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs1962201	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1986694	0.87[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs2525105	0.87[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs3764393	0.80[ASN][1000 genomes]
rs55956628	0.83[ASN][1000 genomes]
rs56006220	0.84[ASN][1000 genomes]
rs56402159	0.86[ASN][1000 genomes]
rs58848175	0.89[ASN][1000 genomes]
rs61396871	0.88[ASN][1000 genomes]
rs73323310	0.83[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	nsv498122	chr17:45763853-46064327	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv518892	chr17:45887951-46029432	Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv908575	chr17:45957591-46049533	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
4	esv1000014	chr17:46019228-46029457	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2325750	ASB16	cis	cerebellum	SCAN
rs2325750	LEPREL4	cis	cerebellum	SCAN
rs2325750	DHX58	cis	parietal	SCAN
rs2325750	ATXN7L3	cis	cerebellum	SCAN
rs2325750	PNPO	cis	cerebellum	SCAN
rs2325750	ASB16	cis	parietal	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46019600-46027000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr17:46019800-46022600	Weak transcription	Rectal Smooth Muscle	rectum
3	chr17:46019800-46022600	Weak transcription	Right Atrium	heart
4	chr17:46019800-46022800	Weak transcription	Fetal Muscle Trunk	muscle
5	chr17:46019800-46022800	Weak transcription	Gastric	stomach
6	chr17:46019800-46022800	Weak transcription	Psoas Muscle	Psoas
7	chr17:46019800-46023400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr17:46019800-46024000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr17:46019800-46024800	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr17:46019800-46025600	Weak transcription	HSMM	muscle
11	chr17:46019800-46026800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr17:46019800-46026800	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr17:46019800-46026800	Weak transcription	Brain Germinal Matrix	brain
14	chr17:46019800-46026800	Weak transcription	HSMMtube	muscle
15	chr17:46019800-46027400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr17:46019800-46034200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr17:46019800-46047600	Weak transcription	Aorta	Aorta
18	chr17:46020000-46022400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr17:46020000-46022600	Weak transcription	NHLF	lung
20	chr17:46020000-46022800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr17:46020000-46022800	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr17:46020000-46024000	Weak transcription	Colon Smooth Muscle	Colon
23	chr17:46020000-46024400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr17:46020000-46026000	Weak transcription	Fetal Heart	heart
25	chr17:46020000-46026200	Weak transcription	Fetal Kidney	kidney
26	chr17:46020000-46026400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr17:46020000-46026400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr17:46020000-46026400	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr17:46020000-46026800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr17:46020000-46026800	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr17:46020000-46027000	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr17:46020000-46034600	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr17:46020200-46022400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr17:46020200-46022400	Weak transcription	Brain Substantia Nigra	brain
35	chr17:46020200-46022400	Weak transcription	NH-A	brain
36	chr17:46020200-46022600	Enhancers	Primary T helper cells PMA-I stimulated	--
37	chr17:46020200-46023000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr17:46020200-46026000	Weak transcription	NHDF-Ad	bronchial
39	chr17:46020200-46026200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr17:46020200-46026200	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr17:46020200-46026800	Weak transcription	HUVEC	blood vessel
42	chr17:46020400-46022400	Weak transcription	Primary B cells from cord blood	blood
43	chr17:46020400-46023600	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr17:46020600-46022400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr17:46020600-46022800	Strong transcription	Left Ventricle	heart
46	chr17:46020600-46024800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr17:46020800-46022800	Genic enhancers	Liver	Liver
48	chr17:46020800-46022800	Genic enhancers	Fetal Thymus	thymus
49	chr17:46020800-46024200	Strong transcription	NHEK	skin
50	chr17:46020800-46024400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast

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