Variant report

Variant	rs12757270
Chromosome Location	chr1:86206738-86206739
allele	A/G
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: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1047893	0.87[ASN][1000 genomes]
rs10873716	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10873717	0.85[ASN][1000 genomes]
rs11161649	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11161650	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11161651	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11161654	0.85[ASN][1000 genomes]
rs11161656	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11161657	0.85[ASN][1000 genomes]
rs11161658	0.85[ASN][1000 genomes]
rs11161659	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11161660	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11161661	0.85[ASN][1000 genomes]
rs11161662	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11161663	0.85[ASN][1000 genomes]
rs11161664	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11161665	0.85[ASN][1000 genomes]
rs11161667	0.87[ASN][1000 genomes]
rs12058974	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12063702	0.87[ASN][1000 genomes]
rs12089500	0.83[ASN][1000 genomes]
rs12097932	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12564080	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12566746	0.83[ASN][1000 genomes]
rs12738010	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12739713	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12752817	0.87[ASN][1000 genomes]
rs12756013	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12758511	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1539444	0.81[ASN][1000 genomes]
rs1889919	0.85[ASN][1000 genomes]
rs1889920	0.85[ASN][1000 genomes]
rs2069208	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2389972	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs35438778	0.80[AMR][1000 genomes]
rs3753786	0.83[ASN][1000 genomes]
rs3753789	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3753790	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6576784	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6672312	0.83[ASN][1000 genomes]
rs6689168	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6697535	0.85[ASN][1000 genomes]
rs7518312	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7520491	0.81[ASN][1000 genomes]
rs7554844	0.87[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12757270	ZNHIT6	cis	Esophagus Muscularis	GTEx
rs12757270	C1orf181	Cis_1M	lymphoblastoid	RTeQTL

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	chr1:86205800-86207000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:86206200-86208800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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