Variant report

Variant	rs4756026
Chromosome Location	chr11:45833960-45833961
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	chr11:45833498-45833987	HepG2	liver:	n/a	n/a
2	POLR2A	chr11:45833433-45835840	MCF-7	breast:	n/a	n/a
3	POLR2A	chr11:45832990-45836303	K562	blood:	n/a	n/a
4	POLR2A	chr11:45833918-45835059	SK-N-MC	brain:	n/a	n/a
5	POLR2A	chr11:45833221-45835005	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:45833116..45834874-chr11:45867735..45869641,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000255447	TF binding region
ENSG00000121671	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11038668	1.00[CHB][hapmap];0.88[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap]
rs11038670	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11038671	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11038675	0.81[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11038689	0.89[TSI][hapmap]
rs17787136	0.81[TSI][hapmap]
rs4756029	0.92[ASN][1000 genomes]
rs55758172	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56131686	0.85[AMR][1000 genomes]
rs7121775	0.89[TSI][hapmap]
rs7123390	0.84[TSI][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	nsv897314	chr11:45816020-45965129	Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv897315	chr11:45817637-45838926	Enhancers Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4756026	CRY2	cis	cerebellum	SCAN
rs4756026	MADD	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:45828000-45834200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr11:45828000-45837200	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr11:45828000-45837200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr11:45828600-45834000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr11:45829200-45835000	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr11:45829600-45834000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr11:45829600-45834400	Strong transcription	Esophagus	oesophagus
8	chr11:45829600-45834400	Strong transcription	NHLF	lung
9	chr11:45829600-45834800	Strong transcription	Primary T cells from cord blood	blood
10	chr11:45829600-45834800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr11:45829600-45834800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr11:45829600-45835000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr11:45829600-45835200	Strong transcription	Fetal Stomach	stomach
14	chr11:45829600-45835800	Weak transcription	HSMM	muscle
15	chr11:45829600-45836000	Weak transcription	HepG2	liver
16	chr11:45829800-45834400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr11:45829800-45834600	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr11:45829800-45835400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr11:45830000-45834400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr11:45830000-45834400	Strong transcription	Placenta Amnion	Placenta Amnion
21	chr11:45830000-45834600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr11:45830000-45834600	Weak transcription	Small Intestine	intestine
23	chr11:45830200-45834000	Strong transcription	Fetal Intestine Large	intestine
24	chr11:45830200-45834400	Strong transcription	Sigmoid Colon	Sigmoid Colon
25	chr11:45830200-45834800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr11:45830200-45835000	Strong transcription	Fetal Intestine Small	intestine
27	chr11:45830400-45834200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr11:45830400-45834400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr11:45830600-45834000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr11:45830600-45834200	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr11:45830600-45834400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr11:45830800-45834000	Strong transcription	Left Ventricle	heart
33	chr11:45830800-45834200	Strong transcription	Muscle Satellite Cultured Cells	--
34	chr11:45830800-45834400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr11:45830800-45834400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr11:45831000-45834000	Strong transcription	Primary B cells from peripheral blood	blood
37	chr11:45831000-45834000	Weak transcription	Fetal Brain Male	brain
38	chr11:45831000-45834200	Strong transcription	Colonic Mucosa	Colon
39	chr11:45831000-45834400	Strong transcription	Duodenum Mucosa	Duodenum
40	chr11:45831000-45834400	Strong transcription	Stomach Smooth Muscle	stomach
41	chr11:45831200-45835000	Strong transcription	Fetal Muscle Leg	muscle
42	chr11:45831200-45837600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr11:45831400-45834000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr11:45831400-45834200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr11:45831400-45834800	Weak transcription	K562	blood
46	chr11:45831600-45834200	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr11:45831600-45834200	Strong transcription	Brain Anterior Caudate	brain
48	chr11:45831600-45834200	Strong transcription	Skeletal Muscle Female	skeletal muscle
49	chr11:45831600-45834400	Strong transcription	Brain Hippocampus Middle	brain
50	chr11:45831600-45834600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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