Variant report

Variant	rs2494692
Chromosome Location	chr6:26615223-26615224
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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	chr6:26596096..26597839-chr6:26614965..26617988,3	K562	blood:
5	chr6:26611565..26613102-chr6:26615089..26617603,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000146109	Chromatin interaction

Extended variants
information (count: 117 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:116)

rs_ID	r²[population]
rs1001687	0.82[AFR][1000 genomes]
rs1021372	1.00[YRI][hapmap];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	1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1027204	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10484442	0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs1056667	0.93[YRI][hapmap]
rs1078679	0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes]
rs10946834	0.93[YRI][hapmap]
rs10946835	0.93[YRI][hapmap]
rs12526680	0.89[CHB][hapmap];1.00[JPT][hapmap]
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]
rs1321479	0.88[YRI][hapmap]
rs1321481	0.92[YRI][hapmap]
rs1321482	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs1490488	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1535276	0.89[YRI][hapmap]
rs1570059	0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes]
rs1570060	0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.82[AFR][1000 genomes]
rs1570061	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs1884946	0.93[YRI][hapmap]
rs1884947	0.80[CHB][hapmap]
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	1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2224380	0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs2255070	0.90[YRI][hapmap]
rs2393670	0.93[YRI][hapmap]
rs2451711	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];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]
rs2494700	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2494701	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2504565	1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2504566	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.90[AFR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2504567	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2504571	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];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]
rs2504599	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs2504600	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];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]
rs3736781	0.89[YRI][hapmap]
rs3736782	0.89[YRI][hapmap]
rs3800303	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4368798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4713006	0.93[YRI][hapmap]
rs4713008	0.93[YRI][hapmap]
rs4871	0.93[YRI][hapmap]
rs62394558	0.90[EUR][1000 genomes]
rs6456733	0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs6456734	0.80[AFR][1000 genomes]
rs6456735	0.90[JPT][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes]
rs6903973	0.89[YRI][hapmap]
rs6913462	0.84[AFR][1000 genomes]
rs6913877	0.84[AFR][1000 genomes]
rs6918360	0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes]
rs6918506	0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.84[AFR][1000 genomes]
rs6918854	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs6922824	0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs6924838	0.80[AFR][1000 genomes]
rs6924865	0.93[YRI][hapmap]
rs6925087	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6925895	0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes]
rs6926629	0.85[YRI][hapmap]
rs6930120	0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs6933176	0.93[YRI][hapmap]
rs6940053	0.80[AFR][1000 genomes]
rs6940188	0.80[AFR][1000 genomes]
rs6941022	0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs767471	0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs7753565	0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs7767847	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9295695	0.93[YRI][hapmap]
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]
rs9357010	0.93[YRI][hapmap]
rs9393729	0.93[YRI][hapmap]
rs9461270	0.93[YRI][hapmap]
rs9461271	0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.80[AFR][1000 genomes]
rs9461272	0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs9461273	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];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]
rs9467773	0.92[YRI][hapmap]
rs9467774	0.93[YRI][hapmap]
rs9467779	0.92[YRI][hapmap]
rs9467782	0.93[YRI][hapmap]
rs9467783	0.93[YRI][hapmap]
rs9467788	0.83[YRI][hapmap]
rs9467791	0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.80[AFR][1000 genomes]
rs9467797	0.80[AFR][1000 genomes]
rs9467798	0.86[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.82[AFR][1000 genomes]
rs9467799	0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs9467800	0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];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	0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs2494692	ZNF322	cis	Thyroid	GTEx
rs2494692	HCG11	Cis_1M	lymphoblastoid	RTeQTL
rs2494692	HMGN4	cis	lesional skin	skin_eQTL
rs2494692	ZNF322	cis	Artery Tibial	GTEx
rs2494692	RP11-457M11.2	cis	Nerve Tibial	GTEx
rs2494692	RP11-457M11.2	cis	Artery Tibial	GTEx
rs2494692	ZNF322A	cis	multi-tissue	Pritchard
rs2494692	RP11-457M11.2	cis	Thyroid	GTEx
rs2494692	HMGN4	Cis_1M	lymphoblastoid	RTeQTL
rs2494692	ZNF322	cis	Nerve Tibial	GTEx
rs2494692	RP11-457M11.2	cis	lung	GTEx

Chromatin state (count:24 , 50 per page) page: 1

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	chr6:26613400-26615600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
5	chr6:26614000-26615400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr6:26614000-26615400	Bivalent/Poised TSS	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr6:26614600-26615400	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
8	chr6:26614800-26615400	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
9	chr6:26615000-26615400	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr6:26615000-26615400	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr6:26615000-26615400	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
12	chr6:26615000-26615400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
13	chr6:26615000-26615400	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
14	chr6:26615000-26615400	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
15	chr6:26615000-26615400	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
16	chr6:26615000-26615400	Bivalent Enhancer	Fetal Intestine Large	intestine
17	chr6:26615000-26615400	Active TSS	Right Atrium	heart
18	chr6:26615000-26615600	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
19	chr6:26615000-26615600	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
20	chr6:26615200-26615400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
21	chr6:26615200-26615400	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr6:26615200-26615400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
23	chr6:26615200-26615400	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
24	chr6:26615200-26615600	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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