Variant report

Variant	rs28546880
Chromosome Location	chr4:2810525-2810526
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:2805467..2811002-chr4:2816486..2823721,11	MCF-7	breast:
2	chr4:2793663..2796017-chr4:2810077..2811741,2	MCF-7	breast:
3	chr4:2807216..2810880-chr4:2811664..2814785,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000087266	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs392479	0.88[EUR][1000 genomes]
rs438524	0.81[EUR][1000 genomes]
rs7677047	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948659	chr4:1828867-2815632	ZNF genes & repeats Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
2	nsv1005116	chr4:2633935-2812340	Bivalent/Poised TSS Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv878444	chr4:2689449-2861090	Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv470002	chr4:2701098-2836628	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv878445	chr4:2704046-2831383	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv878446	chr4:2710644-2810634	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv878447	chr4:2723531-2831383	Flanking Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv516797	chr4:2723531-2836628	Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
9	nsv878448	chr4:2723531-2846799	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
10	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
11	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
12	nsv878449	chr4:2744480-2831383	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
13	nsv1002517	chr4:2747905-2822017	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS 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	19 gene(s)	inside rSNPs	diseases
14	nsv878450	chr4:2760222-2861090	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
15	nsv593435	chr4:2770772-2881256	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
16	nsv878451	chr4:2785556-2856687	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
17	nsv878452	chr4:2789184-2830076	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
18	nsv1010533	chr4:2792848-2873441	Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
19	nsv461162	chr4:2794320-2846799	Strong transcription Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised 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	14 gene(s)	inside rSNPs	diseases
20	nsv593436	chr4:2794320-2846799	Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
21	esv3413278	chr4:2809804-2811927	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
22	esv3338395	chr4:2810154-2811552	Weak transcription Genic enhancers Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:2796200-2813800	Enhancers	Left Ventricle	heart
2	chr4:2796600-2814600	Enhancers	Stomach Mucosa	stomach
3	chr4:2803000-2810600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr4:2803200-2811600	Enhancers	Right Ventricle	heart
5	chr4:2803200-2813400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr4:2803400-2811600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr4:2803400-2812800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr4:2803400-2819200	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr4:2803600-2812600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr4:2803600-2813000	Weak transcription	Primary T cells from cord blood	blood
11	chr4:2803600-2813200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr4:2803600-2813400	Enhancers	Primary B cells from cord blood	blood
13	chr4:2803800-2813000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr4:2804200-2811400	Weak transcription	HepG2	liver
15	chr4:2804400-2811800	Genic enhancers	Primary monocytes fromperipheralblood	blood
16	chr4:2804400-2811800	Genic enhancers	Spleen	Spleen
17	chr4:2804600-2813800	Genic enhancers	Placenta	Placenta
18	chr4:2805800-2812400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr4:2806000-2814600	Enhancers	Liver	Liver
20	chr4:2807600-2810600	Enhancers	Brain Germinal Matrix	brain
21	chr4:2807600-2811200	Genic enhancers	Primary neutrophils fromperipheralblood	blood
22	chr4:2808000-2811200	Weak transcription	A549	lung
23	chr4:2808000-2811200	Genic enhancers	Monocytes-CD14+_RO01746	blood
24	chr4:2808000-2813400	Enhancers	Adipose Nuclei	Adipose
25	chr4:2808200-2812400	Enhancers	Rectal Mucosa Donor 31	rectum
26	chr4:2808400-2813800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr4:2808600-2811000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr4:2808600-2811800	Genic enhancers	Fetal Muscle Leg	muscle
29	chr4:2808600-2812600	Weak transcription	GM12878-XiMat	blood
30	chr4:2808800-2811000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr4:2808800-2811000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr4:2808800-2811200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr4:2808800-2813200	Weak transcription	Thymus	Thymus
34	chr4:2809000-2811200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr4:2809000-2811200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr4:2809000-2811200	Weak transcription	Primary hematopoietic stem cells	blood
37	chr4:2809000-2811200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr4:2809000-2812400	Weak transcription	Fetal Thymus	thymus
39	chr4:2809000-2813400	Weak transcription	NH-A	brain
40	chr4:2809000-2813400	Weak transcription	Osteobl	bone
41	chr4:2809200-2811200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr4:2809200-2813000	Weak transcription	HUVEC	blood vessel
43	chr4:2809200-2813400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr4:2809200-2813400	Weak transcription	Fetal Kidney	kidney
45	chr4:2809200-2815200	Weak transcription	Fetal Brain Female	brain
46	chr4:2809400-2811000	Weak transcription	Brain Substantia Nigra	brain
47	chr4:2809400-2811200	Weak transcription	Brain Angular Gyrus	brain
48	chr4:2809400-2811200	Weak transcription	Brain Cingulate Gyrus	brain
49	chr4:2809400-2812600	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr4:2809400-2813000	Weak transcription	HSMMtube	muscle

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