Variant report

Variant	rs7532758
Chromosome Location	chr1:86207749-86207750
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:86206067..86207782-chr1:86208846..86210943,3	K562	blood:
2	chr1:86206120..86207782-chr1:86209330..86210943,2	K562	blood:

Variant related genes	Relation type
ENSG00000171502	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1047892	0.88[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1047893	0.92[CEU][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1047895	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10518350	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs10782553	0.82[CEU][hapmap];0.83[JPT][hapmap]
rs10873710	0.82[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.82[TSI][hapmap]
rs10873716	0.85[CEU][hapmap]
rs10873717	0.87[EUR][1000 genomes]
rs1094359	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11161643	0.93[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs11161645	0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs11161651	0.85[CEU][hapmap]
rs11161654	0.88[EUR][1000 genomes]
rs11161657	0.88[EUR][1000 genomes]
rs11161658	0.88[EUR][1000 genomes]
rs11161661	0.88[EUR][1000 genomes]
rs11161663	0.87[EUR][1000 genomes]
rs11161665	0.87[EUR][1000 genomes]
rs11161667	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11578464	0.93[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.93[TSI][hapmap]
rs12063702	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12089500	0.85[EUR][1000 genomes]
rs12128916	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12566746	0.92[CEU][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes]
rs12752817	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1539444	0.93[CEU][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs1764285	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1764288	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1764289	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1764291	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1764292	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1764299	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1775988	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1775990	0.96[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs184340	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1889919	0.88[EUR][1000 genomes]
rs1889920	0.88[EUR][1000 genomes]
rs1928626	0.81[EUR][1000 genomes]
rs2389970	0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs2785081	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2995537	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs313727	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs313729	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs373787	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3753786	0.93[CEU][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs3753789	0.85[CEU][hapmap]
rs3753790	0.85[CEU][hapmap]
rs3767162	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs414618	0.95[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs418979	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs419409	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs424205	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs434853	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs447446	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs450145	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4912441	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4949915	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs61783617	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6667094	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6672312	0.93[CEU][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs6689168	0.84[CEU][hapmap]
rs6689925	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6697535	0.93[CEU][hapmap];0.86[JPT][hapmap];0.88[EUR][1000 genomes]
rs6699497	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs709801	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7520491	0.92[CEU][hapmap]
rs7554844	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs821379	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs821381	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs821386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs821389	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs821393	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs821394	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs821396	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs821401	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs843969	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9324154	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs952837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9700177	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv3391173	chr1:86005637-86337469	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv817212	chr1:86127851-86658426	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv871471	chr1:86143084-86211516	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs7532758	ZNHIT6	cis	Adipose Subcutaneous	GTEx
rs7532758	C1orf181	Cis_1M	lymphoblastoid	RTeQTL
rs7532758	ZNHIT6	cis	lung	GTEx
rs7532758	ZNHIT6	cis	lymphoblastoid	seeQTL
rs7532758	ZNHIT6	cis	Artery Aorta	GTEx
rs7532758	C1orf52	cis	parietal	SCAN
rs7532758	LOC339524	cis	cerebellum	SCAN
rs7532758	ZNHIT6	cis	Esophagus Muscularis	GTEx

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86191600-86210400	Weak transcription	Fetal Lung	lung
2	chr1:86196600-86208200	Weak transcription	Primary hematopoietic stem cells	blood
3	chr1:86199000-86211600	Weak transcription	GM12878-XiMat	blood
4	chr1:86202400-86209400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr1:86205600-86207800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr1:86206200-86208800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr1:86206800-86208000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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