Variant report

Variant	rs2223588
Chromosome Location	chr6:24669945-24669946
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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	chr6:24669773-24670175	ENSG00000249810

No data

Variant related genes	Relation type
ENSG00000112312	Chromatin interaction
ENSG00000112308	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1129644	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1555086	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1555087	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1555088	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1885208	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1885209	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1885210	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1923188	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2056999	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2092404	0.94[GIH][hapmap];0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs2143337	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2143339	0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs2223589	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3181238	0.82[EUR][1000 genomes]
rs3212233	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35178258	0.89[EUR][1000 genomes]
rs3777664	0.90[CHD][hapmap];0.94[GIH][hapmap];0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs3822901	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4397216	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4712839	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4712840	0.86[CEU][hapmap];0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs6931502	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6933328	0.81[CHD][hapmap];0.94[GIH][hapmap];0.84[JPT][hapmap]
rs7752101	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7764633	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs926528	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs926529	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461049	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2223588	TDP2	cis	Esophagus Mucosa	GTEx
rs2223588	KIAA0319	cis	Whole Blood	GTEx
rs2223588	TDP2	cis	Muscle Skeletal	GTEx
rs2223588	ACOT13	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

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

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