Variant report

Variant	rs4656465
Chromosome Location	chr1:165865300-165865301
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	GATA2	chr1:165865237-165866192	HUVEC	blood vessel:	n/a	chr1:165866058-165866065 chr1:165866075-165866082
2	CTCF	chr1:165865220-165865370	HBMEC	blood vessel:	n/a	n/a
3	POLR2A	chr1:165864447-165870499	IMR90	lung:	n/a	n/a
4	POLR2A	chr1:165864937-165866025	HUVEC	blood vessel:	n/a	n/a
5	MXI1	chr1:165863482-165866280	IMR90	lung:	n/a	n/a
6	POLR2A	chr1:165865136-165865943	HUVEC	blood vessel:	n/a	n/a
7	MAFK	chr1:165865298-165866163	IMR90	lung:	n/a	n/a
8	MAZ	chr1:165865258-165869632	IMR90	lung:	n/a	chr1:165865613-165865623 chr1:165869315-165869324 chr1:165868230-165868246
9	POLR2A	chr1:165865130-165865606	Hela-S3	cervix:	n/a	n/a
10	CHD1	chr1:165864264-165870908	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:165795260..165799386-chr1:165863983..165867487,4	K562	blood:
2	chr1:165864751..165867551-chr1:165869428..165872327,2	MCF-7	breast:
3	chr1:165859891..165861620-chr1:165865286..165866899,2	MCF-7	breast:
4	chr1:165795600..165798299-chr1:165863664..165866486,4	MCF-7	breast:
5	chr1:165797029..165799386-chr1:165863557..165867019,3	K562	blood:

Variant related genes	Relation type
UCK2	TF binding region
ENSG00000143183	Chromatin interaction
ENSG00000236364	Chromatin interaction
ENSG00000143179	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10918302	0.91[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs12118019	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12119028	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12569109	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1663841	0.82[ASN][1000 genomes]
rs16852447	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3790654	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3790668	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3790669	0.87[EUR][1000 genomes]
rs3790670	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3790674	0.82[EUR][1000 genomes]
rs4656464	0.93[AFR][1000 genomes]
rs4656467	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4657489	0.87[AFR][1000 genomes]
rs475558	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs504436	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs530717	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs576213	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6426943	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6661905	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6682285	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6687465	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs7520107	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7547020	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs9787031	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][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	esv2756102	chr1:165652342-165877342	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:165854000-165869600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr1:165854400-165865400	Weak transcription	Fetal Lung	lung
3	chr1:165854600-165883000	Weak transcription	Colon Smooth Muscle	Colon
4	chr1:165856400-165869600	Weak transcription	Fetal Kidney	kidney
5	chr1:165856600-165878800	Weak transcription	Small Intestine	intestine
6	chr1:165857800-165865800	Weak transcription	Colonic Mucosa	Colon
7	chr1:165858200-165881200	Strong transcription	Dnd41	blood
8	chr1:165858400-165870000	Strong transcription	K562	blood
9	chr1:165858400-165881000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:165858600-165866800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr1:165858600-165872000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr1:165858600-165872600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr1:165858600-165902400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr1:165859000-165866200	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr1:165859000-165881000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:165859200-165866000	Strong transcription	GM12878-XiMat	blood
17	chr1:165859200-165870400	Strong transcription	Fetal Stomach	stomach
18	chr1:165859200-165871000	Strong transcription	Primary hematopoietic stem cells	blood
19	chr1:165859200-165871200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr1:165859200-165878000	Strong transcription	Hela-S3	cervix
21	chr1:165859200-165880400	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr1:165859200-165881000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr1:165859400-165866800	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr1:165859400-165868000	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr1:165859400-165868400	Strong transcription	Duodenum Mucosa	Duodenum
26	chr1:165859400-165868400	Strong transcription	HepG2	liver
27	chr1:165859400-165871200	Strong transcription	Rectal Mucosa Donor 31	rectum
28	chr1:165859400-165880200	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr1:165859400-165880400	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr1:165859400-165880600	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr1:165859400-165880600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr1:165859600-165870200	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr1:165859600-165870800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr1:165859600-165880600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
35	chr1:165859800-165870600	Strong transcription	Fetal Brain Female	brain
36	chr1:165860000-165880200	Strong transcription	H1 Cell Line	embryonic stem cell
37	chr1:165860400-165867600	Strong transcription	Fetal Intestine Large	intestine
38	chr1:165860400-165869200	Strong transcription	Brain Germinal Matrix	brain
39	chr1:165860400-165870400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr1:165860600-165868200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr1:165861400-165865600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr1:165861400-165867400	Enhancers	Fetal Heart	heart
43	chr1:165861600-165866200	Weak transcription	Brain Angular Gyrus	brain
44	chr1:165861600-165866400	Strong transcription	Thymus	Thymus
45	chr1:165861600-165869800	Weak transcription	Fetal Brain Male	brain
46	chr1:165861800-165869400	Weak transcription	Ovary	ovary
47	chr1:165862000-165871800	Weak transcription	Brain Substantia Nigra	brain
48	chr1:165862200-165867000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
49	chr1:165862400-165865600	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr1:165862400-165867000	Weak transcription	Aorta	Aorta

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