Variant report

Variant	rs4845401
Chromosome Location	chr1:154941593-154941594
allele	C/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	chr1:154939926-154944407	SK-N-MC	brain:	n/a	n/a
2	MXI1	chr1:154940562-154944302	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr1:154940758-154948467	HepG2	liver:	n/a	n/a
4	POLR2A	chr1:154941518-154941721	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr1:154941282-154942149	H1-hESC	embryonic stem cell:	n/a	n/a
6	RAD21	chr1:154941262-154941593	SK-N-SH_RA	brain:	n/a	n/a
7	MAZ	chr1:154941060-154944419	IMR90	lung:	n/a	chr1:154943657-154943667 chr1:154941170-154941186 chr1:154943065-154943075 chr1:154943039-154943049
8	POLR2A	chr1:154941494-154944608	PANC-1	pancreas:	n/a	n/a
9	MXI1	chr1:154941258-154944362	IMR90	lung:	n/a	n/a
10	POLR2A	chr1:154941571-154941789	K562	blood:	n/a	n/a
11	POLR2A	chr1:154941092-154944516	PFSK-1	brain:	n/a	n/a
12	POLR2A	chr1:154939859-154942258	H1-hESC	embryonic stem cell:	n/a	n/a
13	SIN3A	chr1:154941403-154941638	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr1:154941531-154941656	HUVEC	blood vessel:	n/a	n/a
15	POLR2A	chr1:154940599-154942254	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr1:154940944-154941669	K562	blood:	n/a	n/a
17	EP300	chr1:154941251-154941666	SK-N-SH_RA	brain:	n/a	n/a
18	POLR2A	chr1:154940737-154942201	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:154941475..154946229-chr1:155017512..155020891,6	MCF-7	breast:
2	chr1:154939878..154945720-chr1:155033369..155036154,5	MCF-7	breast:
3	chr1:154939910..154941909-chr1:155165314..155168020,2	MCF-7	breast:
4	chr1:154941423..154943081-chr1:155031851..155033563,2	K562	blood:

Variant related genes	Relation type
SHC1	TF binding region
ENSG00000169231	Chromatin interaction
ENSG00000232093	Chromatin interaction
ENSG00000143537	Chromatin interaction
ENSG00000231064	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10796937	1.00[JPT][hapmap]
rs12130132	0.81[AFR][1000 genomes]
rs4845695	0.81[AFR][1000 genomes]
rs72702224	0.81[AFR][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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4845401	PBXIP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 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	chr1:154935400-154942000	Strong transcription	Sigmoid Colon	Sigmoid Colon
3	chr1:154935600-154942000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr1:154935600-154942200	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr1:154935600-154942800	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr1:154935800-154941800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr1:154935800-154941800	Strong transcription	Rectal Mucosa Donor 29	rectum
8	chr1:154935800-154942400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr1:154935800-154942400	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr1:154935800-154942600	Strong transcription	Pancreas	Pancrea
11	chr1:154935800-154942600	Strong transcription	Thymus	Thymus
12	chr1:154936000-154941600	Weak transcription	Fetal Heart	heart
13	chr1:154936000-154942800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr1:154936200-154942000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr1:154936200-154942400	Strong transcription	Primary B cells from cord blood	blood
16	chr1:154936200-154942600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr1:154936400-154941600	Strong transcription	Colonic Mucosa	Colon
18	chr1:154936400-154941600	Strong transcription	Duodenum Mucosa	Duodenum
19	chr1:154936400-154941800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr1:154936400-154941800	Weak transcription	Fetal Brain Female	brain
21	chr1:154936400-154941800	Strong transcription	Fetal Thymus	thymus
22	chr1:154936400-154942000	Weak transcription	Fetal Brain Male	brain
23	chr1:154936400-154942800	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr1:154936600-154943200	Strong transcription	Dnd41	blood
25	chr1:154937200-154941800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr1:154937800-154942200	Strong transcription	Primary T killer memory cells from peripheral blood	blood
27	chr1:154937800-154943800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr1:154938000-154941600	Strong transcription	GM12878-XiMat	blood
29	chr1:154938000-154941800	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr1:154938400-154941600	Strong transcription	Liver	Liver
31	chr1:154938400-154942000	Weak transcription	Fetal Kidney	kidney
32	chr1:154938400-154942000	Strong transcription	Gastric	stomach
33	chr1:154938800-154941600	Genic enhancers	Fetal Muscle Leg	muscle
34	chr1:154939200-154942600	Weak transcription	Psoas Muscle	Psoas
35	chr1:154939400-154943200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr1:154939600-154941600	Strong transcription	K562	blood
37	chr1:154939600-154942800	Weak transcription	Small Intestine	intestine
38	chr1:154939800-154941600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr1:154939800-154941800	Genic enhancers	Lung	lung
40	chr1:154939800-154942000	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
41	chr1:154939800-154942000	Genic enhancers	Placenta Amnion	Placenta Amnion
42	chr1:154939800-154942600	Genic enhancers	Spleen	Spleen
43	chr1:154939800-154945800	Genic enhancers	Primary T cells fromperipheralblood	blood
44	chr1:154940000-154941800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr1:154940000-154941800	Genic enhancers	Placenta	Placenta
46	chr1:154940000-154942000	Genic enhancers	Right Ventricle	heart
47	chr1:154940000-154942200	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
48	chr1:154940000-154942200	Genic enhancers	Stomach Mucosa	stomach
49	chr1:154940000-154942200	Transcr. at gene 5' and 3'	Osteobl	bone
50	chr1:154940000-154942400	Genic enhancers	Esophagus	oesophagus

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