Variant report

Variant	rs1490488
Chromosome Location	chr6:26614808-26614809
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIN3A	chr6:26614112-26614822	H1-hESC	embryonic stem cell:	n/a	n/a
2	RAD21	chr6:26614479-26614868	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTBP2	chr6:26613940-26614937	H1-hESC	embryonic stem cell:	n/a	n/a
4	RAD21	chr6:26614645-26614835	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTCF	chr6:26614680-26614830	WERI-Rb-1	eye:	n/a	n/a
6	CTCF	chr6:26614660-26614810	HBMEC	blood vessel:	n/a	n/a
7	CTCF	chr6:26614660-26614810	HRE	kidney:	n/a	n/a
8	MAX	chr6:26614551-26614983	H1-hESC	embryonic stem cell:	n/a	n/a
9	CTCF	chr6:26614700-26614850	HBMEC	blood vessel:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:26614361..26617141-chr6:26622311..26624459,2	K562	blood:
2	chr6:26602910..26606507-chr6:26613473..26615906,4	K562	blood:
3	chr6:26614100..26616221-chr6:26619322..26620866,2	K562	blood:
4	chr6:26613084..26615086-chr6:27100587..27102227,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000271071	TF binding region
ENSG00000196787	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1001687	0.82[AFR][1000 genomes]
rs1021372	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1021373	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10223789	0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs10223792	0.84[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs1027203	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1027204	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1078679	0.80[AFR][1000 genomes]
rs12663883	0.83[AFR][1000 genomes]
rs12663894	0.83[AFR][1000 genomes]
rs12665431	0.82[AFR][1000 genomes]
rs13207371	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1321482	0.84[AFR][1000 genomes]
rs1570059	0.81[AFR][1000 genomes]
rs1570060	0.82[AFR][1000 genomes]
rs1570061	0.84[AFR][1000 genomes]
rs1884949	0.80[AFR][1000 genomes]
rs1977201	0.82[AFR][1000 genomes]
rs2130657	0.90[AFR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2172007	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2451711	0.90[AFR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2451712	0.90[AFR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2451731	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2451740	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2451741	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2451744	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2451750	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2451751	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2494692	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2494700	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2494701	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2494709	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2494713	0.88[AFR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2494716	0.90[AFR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2498351	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2498380	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2504565	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2504566	0.90[AFR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2504567	0.88[AFR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2504571	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2504592	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2504600	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34453863	0.84[EUR][1000 genomes]
rs3800303	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4368798	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62394558	0.90[EUR][1000 genomes]
rs6456734	0.80[AFR][1000 genomes]
rs6456735	0.82[AFR][1000 genomes]
rs6913462	0.84[AFR][1000 genomes]
rs6913877	0.84[AFR][1000 genomes]
rs6918360	0.84[AFR][1000 genomes]
rs6918506	0.84[AFR][1000 genomes]
rs6918854	0.84[AFR][1000 genomes]
rs6924838	0.80[AFR][1000 genomes]
rs6925087	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6925895	0.80[AFR][1000 genomes]
rs6940053	0.80[AFR][1000 genomes]
rs6940188	0.80[AFR][1000 genomes]
rs7767847	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9295698	0.80[AFR][1000 genomes]
rs9295701	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9461271	0.80[AFR][1000 genomes]
rs9461272	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs9461273	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9461275	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9461276	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9467791	0.80[AFR][1000 genomes]
rs9467797	0.80[AFR][1000 genomes]
rs9467798	0.82[AFR][1000 genomes]
rs9467799	0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs9467800	0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs9467802	0.83[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9467804	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9467805	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9467810	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9467813	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9986382	0.80[AFR][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	nsv948921	chr6:26556890-27443957	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	472 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs1490488	RP11-457M11.2	cis	Nerve Tibial	GTEx
rs1490488	RP11-457M11.2	cis	Artery Tibial	GTEx
rs1490488	ZNF322	cis	Nerve Tibial	GTEx
rs1490488	ZNF322A	cis	multi-tissue	Pritchard
rs1490488	HMGN4	Cis_1M	lymphoblastoid	RTeQTL
rs1490488	RP11-457M11.2	cis	lung	GTEx
rs1490488	ZNF322	cis	Artery Tibial	GTEx
rs1490488	RP11-457M11.2	cis	Thyroid	GTEx
rs1490488	ZNF322	cis	Thyroid	GTEx
rs1490488	HCG11	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26612600-26615600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr6:26613200-26615400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
3	chr6:26613200-26615600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
4	chr6:26613400-26615000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
5	chr6:26613400-26615000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
6	chr6:26613400-26615000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
7	chr6:26613400-26615000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
8	chr6:26613400-26615000	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr6:26613400-26615200	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
10	chr6:26613400-26615200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
11	chr6:26613400-26615600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
12	chr6:26613800-26615000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
13	chr6:26613800-26615000	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
14	chr6:26613800-26615000	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
15	chr6:26613800-26615000	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
16	chr6:26613800-26615000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr6:26613800-26615000	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
18	chr6:26613800-26615200	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
19	chr6:26614000-26615000	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr6:26614000-26615000	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr6:26614000-26615000	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr6:26614000-26615000	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr6:26614000-26615000	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
24	chr6:26614000-26615000	Flanking Bivalent TSS/Enh	Primary T helper 17 cells PMA-I stimulated	--
25	chr6:26614000-26615000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr6:26614000-26615000	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
27	chr6:26614000-26615000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr6:26614000-26615000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr6:26614000-26615000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr6:26614000-26615000	Bivalent/Poised TSS	Brain Angular Gyrus	brain
31	chr6:26614000-26615000	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
32	chr6:26614000-26615000	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
33	chr6:26614000-26615000	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
34	chr6:26614000-26615000	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
35	chr6:26614000-26615000	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
36	chr6:26614000-26615000	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
37	chr6:26614000-26615000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
38	chr6:26614000-26615000	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
39	chr6:26614000-26615000	Bivalent/Poised TSS	Fetal Kidney	kidney
40	chr6:26614000-26615000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
41	chr6:26614000-26615000	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
42	chr6:26614000-26615000	Flanking Active TSS	Right Atrium	heart
43	chr6:26614000-26615000	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
44	chr6:26614000-26615000	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
45	chr6:26614000-26615200	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr6:26614000-26615200	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
47	chr6:26614000-26615200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr6:26614000-26615400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr6:26614000-26615400	Bivalent/Poised TSS	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr6:26614200-26615000	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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