Variant report

Variant	rs28439030
Chromosome Location	chr17:46180610-46180611
allele	A/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	NFYB	chr17:46180342-46180762	GM12878	blood:	n/a	chr17:46180478-46180493 chr17:46180503-46180518 chr17:46180545-46180560
2	MAFK	chr17:46180553-46180614	K562	blood:	n/a	n/a
3	SP1	chr17:46180327-46180823	GM12878	blood:	n/a	n/a
4	NFYA	chr17:46180287-46180708	K562	blood:	n/a	chr17:46180548-46180566 chr17:46180572-46180590
5	SP1	chr17:46180266-46180816	K562	blood:	n/a	n/a
6	SP1	chr17:46180283-46180829	GM12878	blood:	n/a	n/a
7	NFYB	chr17:46180346-46180759	K562	blood:	n/a	chr17:46180478-46180493 chr17:46180503-46180518 chr17:46180545-46180560
8	SP1	chr17:46180315-46180746	H1-hESC	embryonic stem cell:	n/a	n/a
9	MAFK	chr17:46180052-46180688	IMR90	lung:	n/a	chr17:46180551-46180566 chr17:46180484-46180499
10	SP1	chr17:46180266-46180720	H1-hESC	embryonic stem cell:	n/a	n/a
11	MAFF	chr17:46180070-46180715	HepG2	liver:	n/a	chr17:46180241-46180259 chr17:46180190-46180208
12	NFYB	chr17:46180485-46180610	Hela-S3	cervix:	n/a	chr17:46180503-46180518 chr17:46180545-46180560
13	CBX3	chr17:46180352-46180913	K562	blood:	n/a	n/a
14	SETDB1	chr17:46180192-46180844	U2OS	brain:	n/a	n/a
15	MYC	chr17:46180475-46180615	K562	blood:	n/a	n/a
16	SP1	chr17:46180246-46180790	A549	lung:	n/a	n/a
17	MAFK	chr17:46180045-46180708	HepG2	liver:	n/a	chr17:46180551-46180566 chr17:46180484-46180499
18	NFYA	chr17:46180406-46180621	GM12878	blood:	n/a	chr17:46180548-46180566 chr17:46180572-46180590
19	MAFK	chr17:46180032-46180697	HepG2	liver:	n/a	chr17:46180551-46180566 chr17:46180484-46180499

No.	Distal block	Cell Line	Cell type
1	chr17:46122869..46127022-chr17:46176971..46180616,11	MCF-7	breast:
2	chr17:46123351..46126971-chr17:46177351..46182209,7	K562	blood:
3	chr17:46174648..46181471-chr17:46183317..46187457,20	MCF-7	breast:
4	chr17:46177349..46182213-chr17:46183318..46186399,5	K562	blood:
5	chr17:46177349..46180853-chr17:46182060..46186447,10	K562	blood:

Variant related genes	Relation type
CBX1	TF binding region
SNX11	TF binding region
ENSG00000263412	Chromatin interaction
ENSG00000082641	Chromatin interaction
ENSG00000002919	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs11079815	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11079817	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11870317	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12452103	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1349676	0.80[EUR][1000 genomes]
rs1452661	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs188268	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1910574	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs208006	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs208007	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs208013	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs208017	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2123342	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2325886	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28551638	0.81[EUR][1000 genomes]
rs2924255	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2924256	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2924258	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2938471	0.82[ASN][1000 genomes]
rs2938480	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2938482	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2957932	0.82[ASN][1000 genomes]
rs2957933	0.82[ASN][1000 genomes]
rs3792693	0.85[EUR][1000 genomes]
rs4794426	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4794427	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4794467	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5016303	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs595874	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6504100	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6504101	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6504113	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7207270	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7208796	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7213530	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7216766	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7220940	0.88[AFR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7225140	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8066529	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8071262	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8077814	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8079982	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8081199	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8182234	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs979746	0.82[ASN][1000 genomes]
rs9893405	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9905460	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469808	chr17:46049868-46228673	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
2	nsv482897	chr17:46049868-46228673	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
3	nsv908576	chr17:46147807-46260366	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46178400-46184200	Weak transcription	Fetal Heart	heart
2	chr17:46179200-46180800	Enhancers	Primary hematopoietic stem cells short term culture	blood
3	chr17:46179200-46180800	Weak transcription	Brain Substantia Nigra	brain
4	chr17:46179200-46181000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr17:46179200-46181000	Enhancers	Primary T killer memory cells from peripheral blood	blood
6	chr17:46179200-46181200	Enhancers	Primary hematopoietic stem cells	blood
7	chr17:46179200-46181800	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr17:46179200-46183800	Weak transcription	Brain Hippocampus Middle	brain
9	chr17:46179200-46184000	Weak transcription	Spleen	Spleen
10	chr17:46179200-46184000	Weak transcription	HepG2	liver
11	chr17:46179200-46184200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr17:46179200-46184200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr17:46179200-46184200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr17:46179200-46184200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr17:46179200-46184200	Weak transcription	Fetal Muscle Trunk	muscle
16	chr17:46179200-46184200	Weak transcription	Left Ventricle	heart
17	chr17:46179200-46184200	Weak transcription	Pancreas	Pancrea
18	chr17:46179200-46184200	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr17:46179200-46184400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr17:46179400-46182400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr17:46179400-46183800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr17:46179400-46184000	Weak transcription	Stomach Smooth Muscle	stomach
23	chr17:46179400-46184200	Weak transcription	Primary T cells from cord blood	blood
24	chr17:46179400-46184200	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr17:46179400-46184200	Weak transcription	Colonic Mucosa	Colon
26	chr17:46179400-46184200	Weak transcription	Duodenum Mucosa	Duodenum
27	chr17:46179400-46184200	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr17:46179600-46180800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr17:46179600-46180800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr17:46179600-46180800	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr17:46179600-46183800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr17:46179600-46184000	Weak transcription	Liver	Liver
33	chr17:46179600-46184000	Weak transcription	Dnd41	blood
34	chr17:46179600-46184000	Weak transcription	Hela-S3	cervix
35	chr17:46179600-46184200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr17:46179600-46184200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr17:46179600-46184200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr17:46179600-46184200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr17:46179600-46184200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr17:46179600-46184200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr17:46179600-46184200	Weak transcription	Brain Cingulate Gyrus	brain
42	chr17:46179600-46184200	Weak transcription	Colon Smooth Muscle	Colon
43	chr17:46179600-46184200	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr17:46179600-46184200	Weak transcription	NHEK	skin
45	chr17:46179600-46184400	Weak transcription	NHDF-Ad	bronchial
46	chr17:46179800-46184400	Weak transcription	Small Intestine	intestine
47	chr17:46180400-46181000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
48	chr17:46180400-46181000	Enhancers	Primary B cells from cord blood	blood
49	chr17:46180400-46181000	ZNF genes & repeats	Primary B cells from peripheral blood	blood
50	chr17:46180400-46182400	Enhancers	Primary T cells fromperipheralblood	blood

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