Variant report

Variant	rs9258260
Chromosome Location	chr6:29723161-29723162
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	PBX3	chr6:29723142-29723377	GM12878	blood:	n/a	n/a
2	BCL3	chr6:29723116-29723406	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:29710119..29712623-chr6:29721345..29723379,2	MCF-7	breast:
2	chr6:29721433..29724421-chr6:29794290..29797232,2	MCF-7	breast:
3	chr6:29721629..29723965-chr6:29782354..29784325,2	K562	blood:

Variant related genes	Relation type
ENSG00000272236	TF binding region
IFITM4P	TF binding region
ENSG00000229142	Chromatin interaction
ENSG00000204632	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1633066	0.89[ASN][1000 genomes]
rs1736913	0.81[ASN][1000 genomes]
rs1736919	0.80[ASN][1000 genomes]
rs1737069	0.88[ASN][1000 genomes]
rs2072894	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2072896	0.91[ASN][1000 genomes]
rs2075682	0.91[ASN][1000 genomes]
rs2076174	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2272874	0.91[ASN][1000 genomes]
rs3734813	0.91[ASN][1000 genomes]
rs3734815	0.87[ASN][1000 genomes]
rs3736694	0.91[ASN][1000 genomes]
rs3736697	0.91[ASN][1000 genomes]
rs3757324	0.89[ASN][1000 genomes]
rs3757325	0.89[ASN][1000 genomes]
rs3757326	0.89[ASN][1000 genomes]
rs3817826	0.84[ASN][1000 genomes]
rs3823318	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6901686	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6910733	0.87[ASN][1000 genomes]
rs7739360	0.81[ASN][1000 genomes]
rs7739388	0.81[ASN][1000 genomes]
rs7741597	0.91[ASN][1000 genomes]
rs7742523	0.91[ASN][1000 genomes]
rs7751815	0.93[ASN][1000 genomes]
rs7753946	0.88[ASN][1000 genomes]
rs7754692	0.90[ASN][1000 genomes]
rs7755571	0.91[ASN][1000 genomes]
rs7759272	0.81[ASN][1000 genomes]
rs7773358	0.91[ASN][1000 genomes]
rs9258156	0.81[ASN][1000 genomes]
rs9258158	0.88[ASN][1000 genomes]
rs9258160	0.88[ASN][1000 genomes]
rs9258163	0.89[ASN][1000 genomes]
rs9258164	0.89[ASN][1000 genomes]
rs9258166	0.89[ASN][1000 genomes]
rs9258167	0.89[ASN][1000 genomes]
rs9258168	0.89[ASN][1000 genomes]
rs9258169	0.89[ASN][1000 genomes]
rs9258170	0.89[ASN][1000 genomes]
rs9258171	0.89[ASN][1000 genomes]
rs9258172	0.89[ASN][1000 genomes]
rs9258173	0.89[ASN][1000 genomes]
rs9258174	0.89[ASN][1000 genomes]
rs9258175	0.89[ASN][1000 genomes]
rs9258187	0.91[ASN][1000 genomes]
rs9258192	0.91[ASN][1000 genomes]
rs9258203	0.90[ASN][1000 genomes]
rs9258205	0.93[ASN][1000 genomes]
rs9258207	0.93[ASN][1000 genomes]
rs9258211	0.93[ASN][1000 genomes]
rs9258212	0.93[ASN][1000 genomes]
rs9258214	0.93[ASN][1000 genomes]
rs9258215	0.93[ASN][1000 genomes]
rs9258216	0.93[ASN][1000 genomes]
rs9258218	0.93[ASN][1000 genomes]
rs9258223	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9258224	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9258225	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9258226	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9258227	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9258228	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9258229	0.88[ASN][1000 genomes]
rs9258230	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9258236	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9258241	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9258242	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9258244	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9258258	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9258259	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9258262	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9258265	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9258266	0.82[AFR][1000 genomes]
rs9258272	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9258274	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
3	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
4	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
5	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
6	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
7	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
8	nsv10809	chr6:29692573-29794119	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
9	nsv883532	chr6:29703262-29814963	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
10	nsv883534	chr6:29708222-29724310	Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	esv3441842	chr6:29715749-29942950	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Crohn's disease	22412388	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9258260	HLA-F	cis	lymphoblastoid	seeQTL
rs9258260	HLA-F	cis	multi-tissue	Pritchard

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29721000-29723200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:29721000-29723200	Weak transcription	Spleen	Spleen
3	chr6:29721000-29724200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr6:29721000-29725200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:29721200-29723200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr6:29721200-29723200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr6:29721200-29723200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr6:29721200-29723600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr6:29721400-29724600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr6:29721600-29724600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr6:29721600-29725400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr6:29721600-29729400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr6:29721800-29723800	Weak transcription	Duodenum Mucosa	Duodenum
14	chr6:29721800-29724600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr6:29721800-29725400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr6:29721800-29725400	Weak transcription	Hela-S3	cervix
17	chr6:29721800-29725400	Weak transcription	HMEC	breast
18	chr6:29723000-29723200	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
19	chr6:29723000-29723600	Strong transcription	Primary B cells from peripheral blood	blood
20	chr6:29723000-29723800	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr6:29723000-29723800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr6:29723000-29728600	Enhancers	ES-I3 Cell Line	embryonic stem cell

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