Variant report

Variant	rs72964338
Chromosome Location	chr2:128052986-128052987
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	POLR2A	chr2:128051180-128053077	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr2:128052437-128053036	GM12878	blood:	n/a	n/a
3	SPI1	chr2:128052614-128053123	HL-60	blood:	n/a	n/a
4	SPI1	chr2:128052502-128053221	HL-60	blood:	n/a	n/a
5	POLR2A	chr2:128052406-128053088	SK-N-MC	brain:	n/a	n/a
6	CUX1	chr2:128052888-128053054	GM12878	blood:	n/a	n/a
7	POLR2A	chr2:128052607-128053020	K562	blood:	n/a	n/a
8	POLR2A	chr2:128052946-128053191	K562	blood:	n/a	n/a
9	POLR2A	chr2:128052888-128053331	HepG2	liver:	n/a	n/a
10	SPI1	chr2:128052654-128053019	GM12878	blood:	n/a	n/a
11	POLR2A	chr2:128052602-128053125	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:128050445..128053038-chr2:128144842..128147674,3	K562	blood:
2	chr2:128050076..128053017-chr2:128173952..128176764,3	MCF-7	breast:

Variant related genes	Relation type
ERCC3	TF binding region
ENSG00000169967	Chromatin interaction
ENSG00000115718	Chromatin interaction
ENSG00000236682	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10169028	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10178188	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10195774	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10206392	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10211382	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10221754	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10439213	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10439214	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10451530	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1128974	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1129121	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13385611	0.80[ASN][1000 genomes]
rs13406313	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13421256	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13424947	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13429050	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13431911	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1607437	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2271026	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3755310	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4150448	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4150487	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4150507	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4150512	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4150515	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55826634	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56276844	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57011781	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57547812	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57878090	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59283013	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59306090	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6710541	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6711086	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6727155	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6740067	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6740368	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6743815	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6750648	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72956480	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72956485	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72964335	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72964344	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72964352	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72964361	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7564189	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7584829	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7586961	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs878461	0.90[EUR][1000 genomes]
rs908787	0.90[EUR][1000 genomes]
rs9808452	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003599	chr2:127871183-128059407	Strong transcription Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv535920	chr2:127871183-128059407	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:128051200-128053000	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr2:128052000-128066200	Weak transcription	Spleen	Spleen
3	chr2:128052200-128053200	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr2:128052200-128062600	Weak transcription	Colon Smooth Muscle	Colon
5	chr2:128052200-128062600	Weak transcription	Fetal Muscle Trunk	muscle
6	chr2:128052200-128062600	Weak transcription	Thymus	Thymus
7	chr2:128052200-128062800	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr2:128052200-128063200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr2:128052200-128063600	Weak transcription	Brain Hippocampus Middle	brain
10	chr2:128052200-128063600	Weak transcription	Left Ventricle	heart
11	chr2:128052200-128063600	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr2:128052200-128063800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr2:128052200-128065000	Weak transcription	Aorta	Aorta
14	chr2:128052200-128065000	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr2:128052200-128066000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr2:128052200-128066200	Weak transcription	Small Intestine	intestine
17	chr2:128052400-128053000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr2:128052400-128053000	Enhancers	Primary B cells from peripheral blood	blood
19	chr2:128052400-128053000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr2:128052400-128053000	Enhancers	Liver	Liver
21	chr2:128052400-128053000	Flanking Active TSS	Dnd41	blood
22	chr2:128052400-128053000	Flanking Active TSS	GM12878-XiMat	blood
23	chr2:128052400-128053000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
24	chr2:128052400-128058600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr2:128052400-128058600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr2:128052400-128059800	Weak transcription	Fetal Lung	lung
27	chr2:128052400-128061800	Weak transcription	Brain Anterior Caudate	brain
28	chr2:128052400-128062000	Weak transcription	Primary T cells from cord blood	blood
29	chr2:128052400-128062600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr2:128052400-128062600	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr2:128052400-128062800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr2:128052400-128062800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr2:128052400-128063000	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr2:128052400-128063200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr2:128052400-128063400	Weak transcription	Psoas Muscle	Psoas
36	chr2:128052400-128063600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr2:128052400-128063600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr2:128052400-128063600	Weak transcription	Fetal Brain Female	brain
39	chr2:128052400-128063600	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr2:128052400-128063800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr2:128052400-128063800	Weak transcription	Brain Substantia Nigra	brain
42	chr2:128052400-128064800	Weak transcription	NH-A	brain
43	chr2:128052400-128065000	Weak transcription	Fetal Stomach	stomach
44	chr2:128052400-128070400	Weak transcription	Esophagus	oesophagus
45	chr2:128052400-128070800	Weak transcription	Colonic Mucosa	Colon
46	chr2:128052400-128071200	Weak transcription	Fetal Brain Male	brain
47	chr2:128052600-128053000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
48	chr2:128052600-128053000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr2:128052600-128053000	Flanking Active TSS	A549	lung
50	chr2:128052600-128053000	Flanking Active TSS	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links