Variant report

Variant	rs11552300
Chromosome Location	chr1:154938954-154938955
allele	A/G
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	chr1:154938954-154939624	HepG2	liver:	n/a	n/a
2	POLR2A	chr1:154938575-154939538	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr1:154938774-154939241	PANC-1	pancreas:	n/a	n/a
4	POLR2A	chr1:154937894-154938998	ECC-1	luminal epithelium:	n/a	n/a
5	POLR2A	chr1:154938934-154939028	MCF-7	breast:	n/a	n/a
6	POLR2A	chr1:154937823-154939133	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr1:154938746-154939091	A549	lung:	n/a	n/a
8	POLR2A	chr1:154937896-154938960	K562	blood:	n/a	n/a
9	POLR2A	chr1:154938657-154939643	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr1:154938495-154939693	PFSK-1	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:154938611..154941490-chr1:155057349..155058983,2	MCF-7	breast:
2	chr1:154937703..154939754-chr1:155022536..155025142,2	MCF-7	breast:

Variant related genes	Relation type
PYGO2	TF binding region
SHC1	TF binding region
ENSG00000143590	Chromatin interaction
ENSG00000143537	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs17356361	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs60445215	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72995438	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72995442	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72995460	0.80[AMR][1000 genomes];0.90[EUR][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	nsv532579	chr1:154548165-155262692	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	575 gene(s)	inside rSNPs	diseases
2	nsv872453	chr1:154904840-154995503	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	147 gene(s)	inside rSNPs	diseases
3	nsv872454	chr1:154904840-155079477	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
4	nsv947546	chr1:154935397-154943641	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154934600-154942800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr1:154935200-154941400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:154935400-154939400	Strong transcription	NHLF	lung
4	chr1:154935400-154939600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr1:154935400-154939600	Strong transcription	Small Intestine	intestine
6	chr1:154935400-154941000	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr1:154935400-154941000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr1:154935400-154942000	Strong transcription	Sigmoid Colon	Sigmoid Colon
9	chr1:154935600-154940000	Strong transcription	Left Ventricle	heart
10	chr1:154935600-154940000	Strong transcription	NH-A	brain
11	chr1:154935600-154940200	Strong transcription	Brain Inferior Temporal Lobe	brain
12	chr1:154935600-154940600	Weak transcription	Right Atrium	heart
13	chr1:154935600-154940800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
14	chr1:154935600-154941000	Strong transcription	H9 Cell Line	embryonic stem cell
15	chr1:154935600-154941000	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr1:154935600-154941000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
17	chr1:154935600-154941200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr1:154935600-154941400	Strong transcription	Aorta	Aorta
19	chr1:154935600-154942000	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr1:154935600-154942200	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr1:154935600-154942800	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr1:154935800-154939200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr1:154935800-154939200	Strong transcription	Psoas Muscle	Psoas
24	chr1:154935800-154939400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr1:154935800-154939600	Strong transcription	Adipose Nuclei	Adipose
26	chr1:154935800-154939800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr1:154935800-154939800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr1:154935800-154940000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr1:154935800-154940600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr1:154935800-154940800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr1:154935800-154940800	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr1:154935800-154940800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr1:154935800-154941000	Strong transcription	Rectal Smooth Muscle	rectum
34	chr1:154935800-154941200	Strong transcription	Fetal Intestine Small	intestine
35	chr1:154935800-154941400	Strong transcription	Fetal Intestine Large	intestine
36	chr1:154935800-154941400	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr1:154935800-154941800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr1:154935800-154941800	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr1:154935800-154942400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr1:154935800-154942400	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr1:154935800-154942600	Strong transcription	Pancreas	Pancrea
42	chr1:154935800-154942600	Strong transcription	Thymus	Thymus
43	chr1:154936000-154939000	Weak transcription	Stomach Mucosa	stomach
44	chr1:154936000-154939800	Strong transcription	Primary T cells from cord blood	blood
45	chr1:154936000-154940000	Strong transcription	Right Ventricle	heart
46	chr1:154936000-154940400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
47	chr1:154936000-154940400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr1:154936000-154940400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr1:154936000-154940400	Strong transcription	A549	lung
50	chr1:154936000-154940600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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