Variant report

Variant	rs9379887
Chromosome Location	chr6:26518662-26518663
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:26170252..26172933-chr6:26517491..26519149,2	K562	blood:
2	chr6:26517743..26520869-chr6:26521157..26524450,4	MCF-7	breast:
3	chr6:26491622..26495206-chr6:26516506..26519658,3	K562	blood:
4	chr6:26271344..26273410-chr6:26517921..26519773,2	MCF-7	breast:
5	chr6:26195075..26199998-chr6:26518402..26523264,7	K562	blood:
6	chr6:26321606..26324992-chr6:26518176..26520933,3	K562	blood:
7	chr6:26215412..26219085-chr6:26518224..26524021,6	K562	blood:

Variant related genes	Relation type
ENSG00000220875	Chromatin interaction
ENSG00000197409	Chromatin interaction
ENSG00000168242	Chromatin interaction
ENSG00000196866	Chromatin interaction
ENSG00000216331	Chromatin interaction
ENSG00000168274	Chromatin interaction
ENSG00000256018	Chromatin interaction
ENSG00000218690	Chromatin interaction
ENSG00000197846	Chromatin interaction
ENSG00000228223	Chromatin interaction
ENSG00000187990	Chromatin interaction

Extended variants
information (count: 118 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs1001687	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs10214634	0.94[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs10223789	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs10223792	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs10484442	0.95[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs1056347	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1056667	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1056668	0.93[EUR][1000 genomes]
rs1078679	0.90[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs10946834	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10946835	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10946837	0.88[EUR][1000 genomes]
rs11752946	0.84[EUR][1000 genomes]
rs11754138	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11756120	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12526680	0.89[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12663883	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12663894	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12665431	0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1321479	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1321480	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1321481	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1321482	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1407045	0.80[EUR][1000 genomes]
rs1535276	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1535277	0.84[AFR][1000 genomes]
rs1570059	0.90[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs1570060	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs1570061	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1884946	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1884947	0.84[EUR][1000 genomes]
rs1884948	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs1884949	0.90[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs1977201	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2024970	0.84[EUR][1000 genomes]
rs2208331	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2224380	0.96[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2255070	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2393669	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2393670	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28558133	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35355150	0.96[EUR][1000 genomes]
rs3736781	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3736782	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3757151	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4573	0.86[EUR][1000 genomes]
rs4713006	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4713008	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4871	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55930917	0.82[EUR][1000 genomes]
rs6456733	0.91[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs6456734	0.93[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6456735	0.89[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs6903973	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6909277	0.83[EUR][1000 genomes]
rs6910899	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6910930	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6913398	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6913462	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs6913877	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs6918360	0.91[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs6918506	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs6918854	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs6922824	0.94[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs6924838	0.90[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6924865	0.85[AFR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6925703	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6925783	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs6925895	0.90[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6926629	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6930120	0.95[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs6932156	0.88[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6932350	0.80[EUR][1000 genomes]
rs6932865	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6933176	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6940053	0.94[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs6940188	0.94[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs6941022	0.96[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs767471	0.96[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9295694	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9295695	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9295698	0.94[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9357010	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9358952	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9358954	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9393728	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9393729	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9393731	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9393732	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9461259	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9461267	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9461270	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9461271	0.94[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9461272	0.89[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs9467773	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9467774	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9467775	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9467776	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9467778	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9467779	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9467782	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9467783	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9467784	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9467787	0.93[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9467791	0.94[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9467796	0.88[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs9467797	0.90[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs9467798	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs9467799	0.89[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs9467800	0.89[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs9467802	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs9467805	0.81[AFR][1000 genomes]
rs9986382	0.94[AFR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
3	nsv1023453	chr6:25853830-26528250	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1201 gene(s)	inside rSNPs	diseases
4	nsv482836	chr6:26352883-26520964	Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv482407	chr6:26369320-26550148	Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9379887	BTN3A3	cis	cerebellar cortex	BrainEAC
rs9379887	HMGN4	Cis_1M	lymphoblastoid	RTeQTL
rs9379887	HCG11	Cis_1M	lymphoblastoid	RTeQTL
rs9379887	HMGN4	cis	Whole Blood	GTEx
rs9379887	ZNF322	cis	Thyroid	GTEx

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26505600-26520600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:26514200-26520400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr6:26515600-26520400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr6:26516000-26520400	Weak transcription	Fetal Intestine Large	intestine
5	chr6:26516000-26520400	Weak transcription	Fetal Intestine Small	intestine
6	chr6:26516200-26520600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr6:26517200-26520600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr6:26517800-26520400	Weak transcription	A549	lung
9	chr6:26518200-26519000	Weak transcription	K562	blood
10	chr6:26518200-26520200	Weak transcription	HepG2	liver

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