Variant report

Variant	rs28490330
Chromosome Location	chr5:43037665-43037666
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SUZ12	chr5:43036692-43038919	H1-hESC	embryonic stem cell:	n/a	n/a
2	TCF12	chr5:43037247-43037681	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr5:43037205-43037804	K562	blood:	n/a	n/a
4	POLR2A	chr5:43036936-43037790	PANC-1	pancreas:	n/a	n/a
5	POLR2A	chr5:43036949-43038717	HL-60	blood:	n/a	n/a
6	CTCF	chr5:43037460-43037750	AG10803	skin:	n/a	n/a
7	RCOR1	chr5:43036862-43039162	IMR90	lung:	n/a	n/a
8	POLR2A	chr5:43036710-43039237	H1-neurons	neurons:	n/a	n/a
9	POLR2A	chr5:43036954-43037819	HL-60	blood:	n/a	n/a
10	POLR2A	chr5:43036958-43037947	H1-neurons	neurons:	n/a	n/a
11	CTBP2	chr5:43037214-43037728	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:43029361..43030941-chr5:43036238..43037788,2	K562	blood:
2	chr5:43029265..43030861-chr5:43036238..43038466,2	K562	blood:
3	chr5:43005892..43011349-chr5:43037590..43043804,20	K562	blood:
4	chr5:43034026..43036831-chr5:43037498..43040104,5	MCF-7	breast:
5	chr5:43013791..43017090-chr5:43037504..43040048,4	K562	blood:
6	chr5:42907582..42909644-chr5:43037324..43039921,2	K562	blood:
7	chr5:43016691..43021968-chr5:43036071..43044426,17	MCF-7	breast:
8	chr5:43014739..43026335-chr5:43034830..43045515,33	MCF-7	breast:
9	chr5:43013791..43016658-chr5:43037504..43040048,3	K562	blood:
10	chr5:43034726..43053192-chr5:43061725..43074206,66	K562	blood:
11	chr5:42967335..42969495-chr5:43037103..43039655,2	K562	blood:
12	chr5:43036901..43050217-chr5:43060442..43069391,53	MCF-7	breast:
13	chr5:43036891..43039253-chr5:43074561..43077276,2	MCF-7	breast:
14	chr5:43008478..43012422-chr5:43036002..43039064,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000215068	TF binding region
ENSG00000272144	Chromatin interaction
ENSG00000251131	Chromatin interaction
ENSG00000271788	Chromatin interaction
ENSG00000177738	Chromatin interaction
ENSG00000251656	Chromatin interaction
ENSG00000172262	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10051990	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10052644	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10054331	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10056822	0.90[AFR][1000 genomes]
rs10057416	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10064210	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs10077219	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13357786	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13357845	1.00[EUR][1000 genomes]
rs13360205	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2085140	0.87[EUR][1000 genomes]
rs28520523	0.87[EUR][1000 genomes]
rs28573681	0.82[AFR][1000 genomes]
rs28609175	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56917209	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs56962140	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs585302	0.96[EUR][1000 genomes]
rs58980582	0.84[EUR][1000 genomes]
rs60608708	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs60859843	0.88[EUR][1000 genomes]
rs6451664	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6451666	0.84[EUR][1000 genomes]
rs673855	1.00[EUR][1000 genomes]
rs6858989	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6859319	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6867941	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6881467	0.93[AMR][1000 genomes]
rs6886261	0.88[EUR][1000 genomes]
rs6890021	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6895961	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6898323	0.88[EUR][1000 genomes]
rs73090747	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7720810	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7725727	0.88[EUR][1000 genomes]
rs7728625	0.80[EUR][1000 genomes]
rs7730865	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7735821	0.92[EUR][1000 genomes]
rs9292865	0.84[EUR][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	nsv993554	chr5:42720939-43251863	Bivalent/Poised TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	298 gene(s)	inside rSNPs	diseases
2	nsv462126	chr5:42728831-43237188	Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
3	nsv597925	chr5:42728831-43237188	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
4	nsv1023741	chr5:42768215-43348145	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
5	nsv537737	chr5:42768215-43348145	Genic enhancers Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
6	nsv534185	chr5:42804840-43067088	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	165 gene(s)	inside rSNPs	diseases
7	nsv1029288	chr5:42928085-43047323	Flanking Bivalent TSS/Enh Active TSS Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	120 gene(s)	inside rSNPs	diseases
8	nsv968169	chr5:42956713-43043472	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	116 gene(s)	inside rSNPs	diseases
9	nsv1024636	chr5:42959979-43295782	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
10	nsv537739	chr5:42959979-43295782	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43020800-43038400	Weak transcription	Spleen	Spleen
2	chr5:43021200-43038600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr5:43035000-43038600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr5:43035200-43039600	Weak transcription	Hela-S3	cervix
5	chr5:43035400-43038000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr5:43035600-43039200	Weak transcription	HepG2	liver
7	chr5:43035800-43039400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr5:43036600-43037800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr5:43036800-43037800	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
10	chr5:43036800-43037800	Flanking Active TSS	HUVEC	blood vessel
11	chr5:43036800-43038200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
12	chr5:43036800-43039000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
13	chr5:43036800-43039600	Active TSS	Placenta	Placenta
14	chr5:43036800-43043800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr5:43037000-43037800	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr5:43037000-43037800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
17	chr5:43037000-43037800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
18	chr5:43037000-43037800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr5:43037000-43037800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
20	chr5:43037000-43037800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
21	chr5:43037000-43037800	ZNF genes & repeats	Right Atrium	heart
22	chr5:43037000-43037800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
23	chr5:43037000-43038000	Flanking Active TSS	Primary T cells from cord blood	blood
24	chr5:43037000-43038000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
25	chr5:43037000-43038000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
26	chr5:43037000-43038000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr5:43037000-43038000	Bivalent/Poised TSS	Fetal Stomach	stomach
28	chr5:43037000-43038000	Flanking Active TSS	NH-A	brain
29	chr5:43037000-43038200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
30	chr5:43037000-43038200	Active TSS	Adipose Nuclei	Adipose
31	chr5:43037000-43038200	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
32	chr5:43037000-43038400	Active TSS	NHDF-Ad	bronchial
33	chr5:43037000-43039000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
34	chr5:43037000-43039000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
35	chr5:43037000-43039000	Flanking Active TSS	NHEK	skin
36	chr5:43037000-43039600	Bivalent/Poised TSS	Left Ventricle	heart
37	chr5:43037000-43040200	Flanking Active TSS	Primary B cells from cord blood	blood
38	chr5:43037000-43040400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr5:43037000-43042200	Bivalent/Poised TSS	Brain Anterior Caudate	brain
40	chr5:43037200-43037800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
41	chr5:43037200-43037800	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
42	chr5:43037200-43037800	Flanking Active TSS	NHLF	lung
43	chr5:43037200-43038000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
44	chr5:43037200-43038000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
45	chr5:43037200-43038000	Enhancers	Gastric	stomach
46	chr5:43037200-43038600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr5:43037200-43038600	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
48	chr5:43037200-43038600	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
49	chr5:43037200-43038800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
50	chr5:43037200-43039000	Flanking Active TSS	Primary B cells from peripheral blood	blood

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