Variant report

Variant	rs2256282
Chromosome Location	chr1:179261902-179261903
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	MYBL2	chr1:179261450-179261993	HepG2	liver:	n/a	n/a
2	RAD21	chr1:179261413-179261945	HepG2	liver:	n/a	chr1:179261621-179261633
3	FOXA2	chr1:179261452-179262004	A549	lung:	n/a	n/a
4	CEBPB	chr1:179261533-179261965	Hela-S3	cervix:	n/a	n/a
5	MAX	chr1:179261432-179261913	Hela-S3	cervix:	n/a	chr1:179261553-179261562
6	RAD21	chr1:179261462-179261988	A549	lung:	n/a	chr1:179261621-179261633
7	CTCF	chr1:179261447-179261987	HCT-116	colon:	n/a	n/a
8	FOS	chr1:179261505-179261912	MCF10A-Er-Src	breast:	n/a	n/a
9	RAD21	chr1:179261275-179262009	SK-N-SH	brain:	n/a	chr1:179261621-179261633
10	SP1	chr1:179261412-179261980	A549	lung:	n/a	chr1:179261494-179261504
11	CTCF	chr1:179261021-179262135	A549	lung:	n/a	n/a
12	ZNF263	chr1:179261481-179261972	HEK293-T-REx	kidney:	n/a	chr1:179261775-179261784
13	MAZ	chr1:179261526-179261921	K562	blood:	n/a	chr1:179261553-179261562
14	RAD21	chr1:179261300-179261992	MCF-7	breast:	n/a	chr1:179261621-179261633
15	RAD21	chr1:179261403-179261916	ECC-1	luminal epithelium:	n/a	chr1:179261621-179261633
16	RAD21	chr1:179261348-179261906	MCF-7	breast:	n/a	chr1:179261621-179261633
17	CTCF	chr1:179261446-179261951	A549	lung:	n/a	n/a
18	RAD21	chr1:179261304-179261931	HCT-116	colon:	n/a	chr1:179261621-179261633
19	MAX	chr1:179261343-179261982	MCF-7	breast:	n/a	chr1:179261553-179261562
20	MYBL2	chr1:179261501-179261998	HepG2	liver:	n/a	n/a
21	RAD21	chr1:179261425-179261931	Hela-S3	cervix:	n/a	chr1:179261621-179261633
22	FOXA2	chr1:179261456-179261958	A549	lung:	n/a	n/a
23	CTCF	chr1:179261411-179261972	MCF-7	breast:	n/a	n/a
24	MBD4	chr1:179261442-179261914	HepG2	liver:	n/a	n/a
25	GATA2	chr1:179261437-179263120	SH-SY5Y	brain:	n/a	chr1:179262475-179262484 chr1:179262389-179262405 chr1:179262475-179262485 chr1:179262393-179262400
26	RAD21	chr1:179261392-179262005	A549	lung:	n/a	chr1:179261621-179261633
27	RAD21	chr1:179261295-179262014	HCT-116	colon:	n/a	chr1:179261621-179261633
28	BHLHE40	chr1:179261544-179261962	K562	blood:	n/a	n/a
29	RFX5	chr1:179261444-179261912	Hela-S3	cervix:	n/a	chr1:179261675-179261692
30	CTCF	chr1:179261394-179262024	SK-N-SH	brain:	n/a	n/a
31	CBX3	chr1:179261420-179261934	K562	blood:	n/a	n/a
32	MAX	chr1:179261493-179261928	Hela-S3	cervix:	n/a	chr1:179261553-179261562
33	GATA1	chr1:179261456-179263358	PBDE	blood:	n/a	chr1:179262475-179262484 chr1:179262389-179262405 chr1:179262475-179262485 chr1:179262393-179262400
34	SMC3	chr1:179261293-179262010	SK-N-SH	brain:	n/a	n/a
35	MAFK	chr1:179261551-179261959	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:179089527..179090473-chr1:179261292..179262134,2	K562	blood:
2	chr1:179220379..179221592-chr1:179260995..179261928,6	MCF-7	breast:
3	chr1:179260885..179265137-chr1:179333383..179339387,7	MCF-7	breast:
4	chr1:179260929..179262434-chr1:179560041..179562229,2	MCF-7	breast:
5	chr1:179049424..179053663-chr1:179259743..179264339,5	MCF-7	breast:
6	chr1:179050855..179052664-chr1:179261724..179264711,2	K562	blood:
7	chr1:179261306..179262860-chr1:179282015..179283875,2	K562	blood:
8	chr1:179074423..179075428-chr1:179261348..179262132,3	MCF-7	breast:
9	chr1:179089981..179090796-chr1:179261194..179262105,4	MCF-7	breast:

Variant related genes	Relation type
SOAT1	TF binding region
ENSG00000162779	Chromatin interaction
ENSG00000162782	Chromatin interaction
ENSG00000186283	Chromatin interaction
ENSG00000263633	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs16853696	0.82[YRI][hapmap]
rs16853718	0.82[YRI][hapmap]
rs17838214	0.82[YRI][hapmap]
rs2244569	1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs2244570	1.00[ASW][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs2246677	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2248847	0.95[AFR][1000 genomes]
rs2250649	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2250753	1.00[AMR][1000 genomes]
rs2251123	0.95[AFR][1000 genomes]
rs2254625	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2484447	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2484448	1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs2493115	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6668333	0.87[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005278	chr1:179197645-179371395	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2256282	RASIP1	trans	lymphoblastoid	seeQTL

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179258400-179262400	Weak transcription	Fetal Kidney	kidney
2	chr1:179258600-179262000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr1:179258600-179262000	Weak transcription	Placenta	Placenta
4	chr1:179258600-179262200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr1:179258600-179262200	Weak transcription	Fetal Intestine Small	intestine
6	chr1:179258600-179262400	Weak transcription	Pancreas	Pancrea
7	chr1:179258600-179262400	Weak transcription	Stomach Mucosa	stomach
8	chr1:179258600-179262600	Weak transcription	Gastric	stomach
9	chr1:179258600-179262600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr1:179258800-179262200	Weak transcription	Fetal Intestine Large	intestine
11	chr1:179258800-179262400	Weak transcription	Colonic Mucosa	Colon
12	chr1:179260800-179262400	Enhancers	Brain Hippocampus Middle	brain
13	chr1:179261400-179262000	Enhancers	Brain Inferior Temporal Lobe	brain
14	chr1:179261400-179262200	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr1:179261400-179262200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr1:179261400-179262200	Enhancers	Liver	Liver
17	chr1:179261400-179262200	Enhancers	Brain Anterior Caudate	brain
18	chr1:179261400-179262200	Enhancers	Rectal Smooth Muscle	rectum
19	chr1:179261400-179262400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr1:179261400-179262400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr1:179261400-179262400	Enhancers	Brain Angular Gyrus	brain
22	chr1:179261400-179262400	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr1:179261600-179262200	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
24	chr1:179261600-179262200	Active TSS	Stomach Smooth Muscle	stomach
25	chr1:179261600-179262200	Flanking Active TSS	HepG2	liver
26	chr1:179261600-179262400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:179261600-179262400	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr1:179261600-179262400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr1:179261600-179262400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
30	chr1:179261600-179262400	Enhancers	Brain Substantia Nigra	brain
31	chr1:179261600-179262400	Enhancers	Duodenum Smooth Muscle	Duodenum
32	chr1:179261800-179262000	Active TSS	Primary hematopoietic stem cells	blood
33	chr1:179261800-179262000	Flanking Active TSS	Brain Cingulate Gyrus	brain
34	chr1:179261800-179262000	Flanking Active TSS	A549	lung
35	chr1:179261800-179262000	Flanking Active TSS	Hela-S3	cervix
36	chr1:179261800-179262200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr1:179261800-179262200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr1:179261800-179262200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr1:179261800-179262200	Enhancers	Duodenum Mucosa	Duodenum
40	chr1:179261800-179262200	Enhancers	Rectal Mucosa Donor 29	rectum
41	chr1:179261800-179262200	Enhancers	K562	blood
42	chr1:179261800-179262200	Enhancers	NH-A	brain
43	chr1:179261800-179262400	Enhancers	Muscle Satellite Cultured Cells	--
44	chr1:179261800-179262800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr1:179261800-179265800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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