Variant report

Variant	rs2790053
Chromosome Location	chr1:165737704-165737705
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:118)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:118 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr1:165737582-165738944	K562	blood:	n/a	n/a
2	SIN3AK20	chr1:165737596-165738670	K562	blood:	n/a	n/a
3	MAZ	chr1:165737623-165738678	Hela-S3	cervix:	n/a	n/a
4	ZMIZ1	chr1:165737377-165739133	K562	blood:	n/a	n/a
5	RCOR1	chr1:165737636-165738954	K562	blood:	n/a	n/a
6	TRIM28	chr1:165737501-165738789	K562	blood:	n/a	n/a
7	POLR2A	chr1:165737551-165739622	HepG2	liver:	n/a	n/a
8	RCOR1	chr1:165737674-165738769	K562	blood:	n/a	n/a
9	GABPA	chr1:165737575-165738780	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr1:165737646-165739273	GM18505	blood:	n/a	n/a
11	POLR2A	chr1:165737685-165738956	PANC-1	pancreas:	n/a	n/a
12	POLR2A	chr1:165737673-165738748	K562	blood:	n/a	n/a
13	MAX	chr1:165737703-165738743	HCT-116	colon:	n/a	n/a
14	STAT3	chr1:165737610-165738208	MCF10A-Er-Src	breast:	n/a	chr1:165738124-165738145
15	POLR2A	chr1:165737524-165739409	GM12878	blood:	n/a	n/a
16	MAX	chr1:165737662-165738717	K562	blood:	n/a	n/a
17	HEY1	chr1:165737636-165738781	K562	blood:	n/a	n/a
18	SMC3	chr1:165737659-165738644	GM12878	blood:	n/a	n/a
19	POLR2A	chr1:165736624-165740514	K562	blood:	n/a	n/a
20	SMC3	chr1:165737641-165738773	Hela-S3	cervix:	n/a	n/a
21	RAD21	chr1:165737645-165738852	IMR90	lung:	n/a	n/a
22	EP300	chr1:165737636-165739039	K562	blood:	n/a	chr1:165738735-165738749
23	EP300	chr1:165737697-165738648	A549	lung:	n/a	n/a
24	POLR2A	chr1:165737685-165739115	Hela-S3	cervix:	n/a	n/a
25	POLR2A	chr1:165737609-165739272	GM12878	blood:	n/a	n/a
26	POLR2A	chr1:165737397-165740059	GM12891	blood:	n/a	n/a
27	MXI1	chr1:165737562-165738710	GM12878	blood:	n/a	n/a
28	STAT5A	chr1:165737546-165738800	GM12878	blood:	n/a	n/a
29	GABPA	chr1:165737609-165738768	HL-60	blood:	n/a	n/a
30	HCFC1	chr1:165736860-165738955	Hela-S3	cervix:	n/a	n/a
31	PML	chr1:165737704-165739135	K562	blood:	n/a	n/a
32	NRF1	chr1:165737569-165738909	GM12878	blood:	n/a	n/a
33	POLR2A	chr1:165737200-165739486	PFSK-1	brain:	n/a	n/a
34	HCFC1	chr1:165737294-165738718	K562	blood:	n/a	n/a
35	TEAD4	chr1:165737571-165739288	K562	blood:	n/a	n/a
36	POLR2A	chr1:165737611-165738997	K562	blood:	n/a	n/a
37	POLR2A	chr1:165737294-165739204	MCF10A-Er-Src	breast:	n/a	n/a
38	ELK4	chr1:165737629-165738700	Hela-S3	cervix:	n/a	chr1:165738120-165738131 chr1:165738144-165738155
39	MYC	chr1:165737448-165738891	K562	blood:	n/a	n/a
40	HEY1	chr1:165737592-165738852	K562	blood:	n/a	n/a
41	MAX	chr1:165737646-165738774	K562	blood:	n/a	n/a
42	MXI1	chr1:165737675-165738898	HepG2	liver:	n/a	n/a
43	BHLHE40	chr1:165737661-165738812	K562	blood:	n/a	n/a
44	POLR2A	chr1:165737558-165739285	MCF10A-Er-Src	breast:	n/a	n/a
45	POLR2A	chr1:165737623-165739441	GM12892	blood:	n/a	n/a
46	PAX5	chr1:165737689-165738529	GM12878	blood:	n/a	n/a
47	ZNF384	chr1:165737524-165738963	K562	blood:	n/a	n/a
48	TAF1	chr1:165737661-165738757	ECC-1	luminal epithelium:	n/a	n/a
49	GABPA	chr1:165737574-165738674	K562	blood:	n/a	n/a
50	MYBL2	chr1:165737682-165738669	HepG2	liver:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:165737640..165738218-chr11:65266056..65266964,2	NB4	blood:
2	chr1:165735886..165744990-chr1:165791702..165805629,42	K562	blood:
3	chr1:149223515..149224444-chr1:165737612..165738441,2	HCT-116	colon:
4	chr1:165736523..165741866-chr1:165791420..165802380,26	K562	blood:
5	chr1:165736117..165742504-chr1:165795129..165799551,11	MCF-7	breast:
6	chr1:165601421..165603432-chr1:165737509..165739117,2	K562	blood:
7	chr1:165735066..165739781-chr1:165794447..165799093,13	MCF-7	breast:
8	chr1:165735880..165737855-chr1:165863441..165866125,2	K562	blood:
9	chr1:165737601..165739848-chr12:7052889..7054535,2	MCF-7	breast:
10	chr1:165667536..165669486-chr1:165736821..165739691,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000224358	TF binding region
ENSG00000238923	Chromatin interaction
ENSG00000272173	Chromatin interaction
ENSG00000143179	Chromatin interaction
ENSG00000143198	Chromatin interaction
ENSG00000215838	Chromatin interaction
ENSG00000206737	Chromatin interaction
ENSG00000143149	Chromatin interaction
ENSG00000143183	Chromatin interaction
ENSG00000251562	Chromatin interaction
ENSG00000111678	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10800135	1.00[JPT][hapmap]
rs10800153	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800154	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10800155	1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10918274	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12133745	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12403369	1.00[JPT][hapmap]
rs12691499	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12691500	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1547725	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs2251768	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs2790049	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2790052	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814463	0.83[ASN][1000 genomes]
rs2814466	1.00[JPT][hapmap]
rs2814471	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28504591	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4233408	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4537525	1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4603103	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4656461	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4657471	1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4657472	0.83[ASN][1000 genomes]
rs4657474	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4657475	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4657476	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4657477	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6426936	0.80[AMR][1000 genomes]
rs6660601	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6662839	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6668108	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6668885	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6696454	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71628393	0.83[ASN][1000 genomes]
rs7518099	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7524755	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7528177	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7555523	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
2	nsv1011720	chr1:165669589-165802516	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv518886	chr1:165714187-165741646	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:165736800-165738000	Flanking Active TSS	Primary T cells from cord blood	blood
2	chr1:165736800-165738000	Flanking Active TSS	Fetal Brain Female	brain
3	chr1:165737000-165737800	Flanking Active TSS	Liver	Liver
4	chr1:165737000-165737800	Flanking Active TSS	Brain Anterior Caudate	brain
5	chr1:165737000-165738000	Flanking Active TSS	Adipose Nuclei	Adipose
6	chr1:165737000-165739200	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr1:165737000-165739400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr1:165737200-165737800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
9	chr1:165737200-165737800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
10	chr1:165737200-165737800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr1:165737200-165737800	Flanking Active TSS	Duodenum Mucosa	Duodenum
12	chr1:165737200-165737800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
13	chr1:165737200-165737800	Flanking Active TSS	HUVEC	blood vessel
14	chr1:165737200-165737800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
15	chr1:165737200-165737800	Flanking Active TSS	Osteobl	bone
16	chr1:165737200-165738000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr1:165737200-165738000	Flanking Active TSS	Primary B cells from cord blood	blood
18	chr1:165737200-165738000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
19	chr1:165737200-165738000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
20	chr1:165737200-165738000	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
21	chr1:165737200-165738000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr1:165737200-165738800	Active TSS	iPS-20b Cell Line	embryonic stem cell
23	chr1:165737200-165739000	Active TSS	H1 Cell Line	embryonic stem cell
24	chr1:165737200-165739000	Active TSS	Fetal Intestine Large	intestine
25	chr1:165737200-165739000	Active TSS	Lung	lung
26	chr1:165737200-165739000	Active TSS	Psoas Muscle	Psoas
27	chr1:165737200-165739200	Active TSS	ES-I3 Cell Line	embryonic stem cell
28	chr1:165737200-165739200	Active TSS	HUES6 Cell Line	embryonic stem cell
29	chr1:165737200-165739200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
30	chr1:165737200-165739200	Active TSS	Right Atrium	heart
31	chr1:165737200-165739400	Active TSS	HUES48 Cell Line	embryonic stem cell
32	chr1:165737200-165739400	Active TSS	iPS-15b Cell Line	embryonic stem cell
33	chr1:165737200-165739600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr1:165737400-165737800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
35	chr1:165737400-165737800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
36	chr1:165737400-165737800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
37	chr1:165737400-165737800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
38	chr1:165737400-165737800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
39	chr1:165737400-165737800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
40	chr1:165737400-165737800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
41	chr1:165737400-165737800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
42	chr1:165737400-165737800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr1:165737400-165737800	Flanking Active TSS	Dnd41	blood
44	chr1:165737400-165738000	Flanking Active TSS	Primary B cells from peripheral blood	blood
45	chr1:165737400-165738000	Flanking Active TSS	Primary hematopoietic stem cells	blood
46	chr1:165737400-165738000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
47	chr1:165737400-165738000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
48	chr1:165737400-165738400	Active TSS	Fetal Thymus	thymus
49	chr1:165737400-165738600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr1:165737400-165738600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links