Variant report

Variant	rs1256430
Chromosome Location	chr15:83519472-83519473
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	SMC3	chr15:83518203-83520477	SK-N-SH	brain:	n/a	chr15:83519746-83519760
2	CTCF	chr15:83518155-83520081	SK-N-SH	brain:	n/a	chr15:83519744-83519762 chr15:83519438-83519446
3	RAD21	chr15:83518188-83520217	SK-N-SH	brain:	n/a	chr15:83519745-83519758 chr15:83519858-83519867 chr15:83519742-83519761 chr15:83519744-83519756

No.	Distal block	Cell Line	Cell type
1	chr15:83477527..83479377-chr15:83517237..83519936,2	K562	blood:
2	chr15:83517113..83521654-chr15:83652714..83657006,7	MCF-7	breast:
3	chr15:83519425..83521228-chr15:83661730..83663571,2	K562	blood:
4	chr15:83516928..83520058-chr15:83678480..83682741,4	K562	blood:
5	chr15:83477529..83479377-chr15:83517237..83520056,3	K562	blood:

Variant related genes	Relation type
HOMER2	TF binding region
ENSG00000169609	Chromatin interaction
ENSG00000169612	Chromatin interaction
ENSG00000260608	Chromatin interaction
ENSG00000156232	Chromatin interaction
ENSG00000103942	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1105287	0.82[GIH][hapmap]
rs11631033	0.82[GIH][hapmap]
rs11635357	0.82[GIH][hapmap]
rs11637448	0.82[GIH][hapmap]
rs11853499	1.00[YRI][hapmap]
rs11857742	1.00[YRI][hapmap]
rs1256433	0.84[CEU][hapmap];0.80[EUR][1000 genomes]
rs12907810	0.87[GIH][hapmap]
rs1553886	0.82[GIH][hapmap]
rs2061948	0.83[CEU][hapmap]
rs3814281	0.87[GIH][hapmap]
rs4132210	0.82[GIH][hapmap]
rs4779061	0.82[GIH][hapmap]

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	nsv469557	chr15:83417763-83560629	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
2	nsv482340	chr15:83417763-83560629	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
3	nsv471687	chr15:83417764-83560629	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1256430	WDR73	cis	parietal	SCAN
rs1256430	CPEB1	cis	parietal	SCAN
rs1256430	HOMER2	cis	parietal	SCAN
rs1256430	WHAMM	cis	parietal	SCAN
rs1256430	RASGRF1	cis	cerebellum	SCAN
rs1256430	SCAND2	cis	parietal	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83504600-83549400	Weak transcription	Psoas Muscle	Psoas
2	chr15:83505800-83520800	Weak transcription	Dnd41	blood
3	chr15:83505800-83522400	Weak transcription	Fetal Kidney	kidney
4	chr15:83506000-83524200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr15:83506200-83527400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr15:83506200-83543800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr15:83507200-83539400	Weak transcription	Fetal Intestine Small	intestine
8	chr15:83507800-83521800	Weak transcription	Brain Germinal Matrix	brain
9	chr15:83513200-83532000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr15:83514200-83521600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr15:83514400-83542800	Weak transcription	Primary T cells from cord blood	blood
12	chr15:83516000-83523400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr15:83517000-83519600	Enhancers	Fetal Muscle Leg	muscle
14	chr15:83517400-83519800	Genic enhancers	Pancreas	Pancrea
15	chr15:83517400-83520200	Enhancers	Fetal Muscle Trunk	muscle
16	chr15:83517800-83519600	Enhancers	Primary hematopoietic stem cells	blood
17	chr15:83517800-83522800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr15:83518000-83519600	Enhancers	Placenta Amnion	Placenta Amnion
19	chr15:83518200-83519600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr15:83518200-83519600	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr15:83518200-83519800	Enhancers	HSMM	muscle
22	chr15:83518200-83522600	Enhancers	Fetal Brain Female	brain
23	chr15:83518200-83523000	Enhancers	Fetal Thymus	thymus
24	chr15:83518400-83519600	Enhancers	Brain Substantia Nigra	brain
25	chr15:83518400-83522800	Enhancers	Fetal Brain Male	brain
26	chr15:83518600-83519600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr15:83518600-83519600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr15:83518600-83519600	Enhancers	NHEK	skin
29	chr15:83518600-83519800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr15:83518600-83520000	Enhancers	Brain Hippocampus Middle	brain
31	chr15:83518600-83520000	Enhancers	Thymus	Thymus
32	chr15:83518600-83520000	Enhancers	Spleen	Spleen
33	chr15:83518600-83520200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
34	chr15:83518600-83520400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr15:83518600-83522400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr15:83518800-83519600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr15:83518800-83520000	Enhancers	Brain Cingulate Gyrus	brain
38	chr15:83518800-83520000	Enhancers	Brain Inferior Temporal Lobe	brain
39	chr15:83518800-83520200	Enhancers	Brain Angular Gyrus	brain
40	chr15:83518800-83520800	Weak transcription	Primary B cells from cord blood	blood
41	chr15:83518800-83521000	Enhancers	Cortex derived primary cultured neurospheres	brain
42	chr15:83518800-83524200	Weak transcription	Lung	lung
43	chr15:83519000-83519600	Enhancers	HepG2	liver
44	chr15:83519000-83519600	Enhancers	HMEC	breast
45	chr15:83519000-83519600	Enhancers	HSMMtube	muscle
46	chr15:83519000-83519600	Enhancers	K562	blood
47	chr15:83519000-83519800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr15:83519000-83519800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr15:83519000-83519800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr15:83519000-83519800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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