Variant report

Variant	rs2223589
Chromosome Location	chr6:24669472-24669473
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	IRF1	chr6:24668580-24669888	K562	blood:	n/a	chr6:24669183-24669204
2	POLR2A	chr6:24666488-24669678	K562	blood:	n/a	n/a
3	MAX	chr6:24668475-24669606	K562	blood:	n/a	n/a
4	POLR2A	chr6:24668490-24669593	HL-60	blood:	n/a	n/a
5	EP300	chr6:24668623-24669730	K562	blood:	n/a	n/a
6	MYC	chr6:24668467-24669703	K562	blood:	n/a	n/a
7	POLR2A	chr6:24666499-24669700	K562	blood:	n/a	n/a
8	POLR2A	chr6:24666489-24669560	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:24666490..24670247-chr6:24774150..24780460,9	K562	blood:
2	chr6:24665480..24670247-chr6:24773496..24779775,9	K562	blood:
3	chr6:24668894..24670488-chr6:24670506..24672451,2	K562	blood:
4	chr6:24660920..24672880-chr6:24713381..24723000,42	K562	blood:
5	chr6:24668887..24670760-chr6:26011483..26013160,2	K562	blood:
6	chr6:24661385..24670379-chr6:24713871..24722680,32	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TDP2-1	chr6:24667807-24669720	ENSG00000249810

No data

Variant related genes	Relation type
TDP2	TF binding region
ENSG00000112312	Chromatin interaction
ENSG00000112308	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1129644	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1555086	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1555087	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1555088	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1885208	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1885209	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1885210	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1923188	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2056999	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2092404	0.80[ASN][1000 genomes]
rs2143337	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2143339	0.84[EUR][1000 genomes]
rs2223588	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3181238	0.84[EUR][1000 genomes]
rs3212233	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35178258	0.91[EUR][1000 genomes]
rs3777664	0.80[ASN][1000 genomes]
rs3822901	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4397216	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4712839	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4712840	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6931502	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7752101	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7764633	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs926528	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs926529	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461049	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[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	esv3508002	chr6:24618580-24732946	Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	esv3508003	chr6:24618580-24732946	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2223589	TDP2	cis	Muscle Skeletal	GTEx
rs2223589	KIAA0319	cis	Whole Blood	GTEx
rs2223589	TDP2	cis	Esophagus Mucosa	GTEx

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24665800-24669800	Active TSS	A549	lung
2	chr6:24666000-24669600	Active TSS	K562	blood
3	chr6:24668000-24676000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr6:24668200-24669600	Enhancers	Primary T cells fromperipheralblood	blood
5	chr6:24668200-24669600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr6:24668200-24670200	ZNF genes & repeats	Fetal Intestine Small	intestine
7	chr6:24668200-24674400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr6:24668200-24699800	Weak transcription	Brain Substantia Nigra	brain
9	chr6:24668400-24671800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr6:24668600-24671000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr6:24668800-24669600	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
12	chr6:24668800-24669600	Active TSS	Rectal Mucosa Donor 29	rectum
13	chr6:24668800-24669800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
14	chr6:24668800-24670200	Strong transcription	H1 Cell Line	embryonic stem cell
15	chr6:24668800-24670600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr6:24668800-24672400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
17	chr6:24668800-24691800	Weak transcription	Psoas Muscle	Psoas
18	chr6:24669000-24669600	Enhancers	HepG2	liver
19	chr6:24669000-24672800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr6:24669000-24673000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr6:24669000-24675800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr6:24669000-24681800	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr6:24669000-24686400	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr6:24669000-24690400	Weak transcription	Gastric	stomach
25	chr6:24669000-24693000	Weak transcription	Primary T cells from cord blood	blood
26	chr6:24669000-24701200	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr6:24669200-24669600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr6:24669200-24670800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr6:24669200-24675800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
30	chr6:24669200-24686200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr6:24669200-24690800	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr6:24669400-24669600	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
33	chr6:24669400-24669800	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
34	chr6:24669400-24669800	Active TSS	Hela-S3	cervix
35	chr6:24669400-24670000	Flanking Active TSS	Liver	Liver
36	chr6:24669400-24671200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr6:24669400-24687600	Weak transcription	Left Ventricle	heart
38	chr6:24669400-24701600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links