Variant report

Variant	rs9258172
Chromosome Location	chr6:29689973-29689974
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	chr6:29689319..29693460-chr6:29694038..29698697,5	MCF-7	breast:
2	chr6:29689852..29692667-chr6:31324164..31326641,2	K562	blood:

Variant related genes	Relation type
ENSG00000271581	Chromatin interaction
ENSG00000239257	Chromatin interaction
ENSG00000234745	Chromatin interaction

Extended variants
information (count: 112 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs1476573	0.80[ASN][1000 genomes]
rs1610584	0.80[ASN][1000 genomes]
rs1610586	0.80[ASN][1000 genomes]
rs1610587	0.80[ASN][1000 genomes]
rs1610590	0.80[ASN][1000 genomes]
rs1610592	0.80[ASN][1000 genomes]
rs1610593	0.80[ASN][1000 genomes]
rs1610594	0.80[ASN][1000 genomes]
rs1610595	0.80[ASN][1000 genomes]
rs1610745	0.80[ASN][1000 genomes]
rs1611356	0.80[ASN][1000 genomes]
rs1611357	0.80[ASN][1000 genomes]
rs1611363	0.80[ASN][1000 genomes]
rs1611365	0.80[ASN][1000 genomes]
rs1611366	0.80[ASN][1000 genomes]
rs1611369	0.80[ASN][1000 genomes]
rs1611370	0.80[ASN][1000 genomes]
rs1611372	0.80[ASN][1000 genomes]
rs1611375	0.80[ASN][1000 genomes]
rs1611376	0.80[ASN][1000 genomes]
rs1611377	0.80[ASN][1000 genomes]
rs1611378	0.80[ASN][1000 genomes]
rs1611379	0.80[ASN][1000 genomes]
rs1627465	0.81[ASN][1000 genomes]
rs1736913	0.83[ASN][1000 genomes]
rs1736919	0.87[ASN][1000 genomes]
rs1736930	0.80[ASN][1000 genomes]
rs2072894	0.91[ASN][1000 genomes]
rs2072896	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2075682	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2076174	0.91[ASN][1000 genomes]
rs2272874	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3116789	0.80[ASN][1000 genomes]
rs3116790	0.80[ASN][1000 genomes]
rs3131863	0.80[ASN][1000 genomes]
rs3734813	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3734815	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3736694	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3736697	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3757324	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3757325	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3757326	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3817826	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3823318	0.89[ASN][1000 genomes]
rs6901686	0.91[ASN][1000 genomes]
rs6910733	0.91[AFR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7738786	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7739360	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7739388	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7741597	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7742523	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7751815	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7753946	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7754692	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7755571	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7759272	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7773358	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9258156	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9258158	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9258160	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9258163	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9258164	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9258166	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9258167	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9258168	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9258169	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9258170	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9258171	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9258173	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9258174	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9258175	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9258176	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9258187	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9258192	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9258203	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9258205	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9258207	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9258211	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9258212	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9258214	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9258215	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9258216	0.94[ASN][1000 genomes]
rs9258218	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9258223	0.86[ASN][1000 genomes]
rs9258224	0.89[ASN][1000 genomes]
rs9258225	0.91[ASN][1000 genomes]
rs9258226	0.86[ASN][1000 genomes]
rs9258227	0.86[ASN][1000 genomes]
rs9258228	0.81[ASN][1000 genomes]
rs9258229	0.81[ASN][1000 genomes]
rs9258230	0.91[ASN][1000 genomes]
rs9258236	0.91[ASN][1000 genomes]
rs9258241	0.90[ASN][1000 genomes]
rs9258242	0.91[ASN][1000 genomes]
rs9258244	0.89[ASN][1000 genomes]
rs9258258	0.89[ASN][1000 genomes]
rs9258259	0.89[ASN][1000 genomes]
rs9258260	0.89[ASN][1000 genomes]
rs9258262	0.89[ASN][1000 genomes]
rs9258265	0.89[ASN][1000 genomes]
rs9258272	0.87[ASN][1000 genomes]
rs9258274	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv20940	chr6:29653954-29923410	Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv970675	chr6:29657036-29692268	Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv428475	chr6:29659525-29763392	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv428139	chr6:29659525-29892317	Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
5	nsv427749	chr6:29659525-29975144	Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
6	nsv508397	chr6:29663132-29761448	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
7	esv1821077	chr6:29670915-29726207	Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	esv1794141	chr6:29670915-29765814	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
9	nsv462673	chr6:29689590-29700183	Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv601230	chr6:29689590-29700183	Flanking Active TSS Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9258172	HLA-F	cis	multi-tissue	Pritchard
rs9258172	HLA-F-AS1	cis	Artery Aorta	GTEx
rs9258172	HLA-F-AS1	cis	Thyroid	GTEx
rs9258172	HLA-F-AS1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29664000-29690600	Weak transcription	Right Atrium	heart
2	chr6:29688200-29690400	Enhancers	Primary T cells fromperipheralblood	blood
3	chr6:29688400-29690200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr6:29688400-29690200	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr6:29688400-29690200	Enhancers	Primary T killer memory cells from peripheral blood	blood
6	chr6:29688400-29690400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr6:29688600-29690800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr6:29689200-29690000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
9	chr6:29689200-29690000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr6:29689200-29690400	Enhancers	Primary B cells from peripheral blood	blood
11	chr6:29689200-29690400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
12	chr6:29689200-29690400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr6:29689400-29690200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
14	chr6:29689400-29690800	Weak transcription	Spleen	Spleen
15	chr6:29689600-29690000	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr6:29689600-29690000	Flanking Active TSS	GM12878-XiMat	blood
17	chr6:29689600-29690400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr6:29689600-29690600	Enhancers	Primary B cells from cord blood	blood
19	chr6:29689800-29690000	Enhancers	Primary T cells from cord blood	blood
20	chr6:29689800-29690000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
21	chr6:29689800-29690000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
22	chr6:29689800-29690000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
23	chr6:29689800-29690200	Enhancers	Duodenum Mucosa	Duodenum

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