Variant report

Variant	rs28656878
Chromosome Location	chr4:2816529-2816530
allele	A/C
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	POLR2A	chr4:2816462-2817330	GM12891	blood:	n/a	n/a
2	POLR2A	chr4:2815877-2816601	GM12878	blood:	n/a	n/a
3	STAT5A	chr4:2816252-2817072	GM12878	blood:	n/a	chr4:2816479-2816491
4	POLR2A	chr4:2816317-2817766	HL-60	blood:	n/a	n/a
5	POLR2A	chr4:2816515-2817431	GM12892	blood:	n/a	n/a
6	POLR2A	chr4:2816477-2816864	GM12891	blood:	n/a	n/a
7	STAT5A	chr4:2816276-2816797	GM12878	blood:	n/a	chr4:2816479-2816491

No.	Distal block	Cell Line	Cell type
1	chr4:2815555..2818329-chr4:2819380..2822501,3	MCF-7	breast:
2	chr4:2811128..2813446-chr4:2813847..2818794,5	MCF-7	breast:
3	chr4:2793845..2803067-chr4:2816443..2823671,22	MCF-7	breast:
4	chr4:2794084..2803742-chr4:2816227..2824357,23	MCF-7	breast:
5	chr4:2815294..2817110-chr4:2817843..2820313,2	K562	blood:

Variant related genes	Relation type
SH3BP2	TF binding region
ENSG00000087266	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs9994090	1.00[AFR][1000 genomes]
rs9996929	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:2803400-2819200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr4:2811800-2819400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr4:2813400-2817200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr4:2813800-2818800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:2813800-2819000	Weak transcription	Brain Cingulate Gyrus	brain
6	chr4:2814200-2817200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr4:2814200-2817400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr4:2814800-2816600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
9	chr4:2814800-2819000	Weak transcription	Fetal Lung	lung
10	chr4:2814800-2819200	Weak transcription	NH-A	brain
11	chr4:2814800-2819400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr4:2815200-2816600	Enhancers	Primary hematopoietic stem cells	blood
13	chr4:2815200-2817400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr4:2815200-2817400	Genic enhancers	Gastric	stomach
15	chr4:2815200-2817400	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
16	chr4:2815200-2817600	Genic enhancers	Placenta	Placenta
17	chr4:2815200-2817800	Genic enhancers	Primary monocytes fromperipheralblood	blood
18	chr4:2815200-2818800	Weak transcription	Fetal Intestine Large	intestine
19	chr4:2815200-2819000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr4:2815200-2819200	Weak transcription	Small Intestine	intestine
21	chr4:2815200-2819200	Weak transcription	NHLF	lung
22	chr4:2815400-2816600	Transcr. at gene 5' and 3'	Primary B cells from cord blood	blood
23	chr4:2815400-2817000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr4:2815400-2817000	Genic enhancers	Liver	Liver
25	chr4:2815400-2817200	Strong transcription	Fetal Intestine Small	intestine
26	chr4:2815400-2817400	Enhancers	Fetal Thymus	thymus
27	chr4:2815400-2817600	Genic enhancers	Primary neutrophils fromperipheralblood	blood
28	chr4:2815400-2817600	Genic enhancers	Lung	lung
29	chr4:2815400-2817600	Genic enhancers	Spleen	Spleen
30	chr4:2815400-2817800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr4:2815400-2818000	Weak transcription	Brain Hippocampus Middle	brain
32	chr4:2815400-2819000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr4:2815400-2819200	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr4:2815400-2819200	Weak transcription	Rectal Smooth Muscle	rectum
35	chr4:2815400-2819200	Weak transcription	HSMM	muscle
36	chr4:2815400-2819200	Weak transcription	HSMMtube	muscle
37	chr4:2815400-2819600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr4:2815600-2816600	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr4:2815600-2816800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr4:2815600-2816800	Enhancers	Stomach Smooth Muscle	stomach
41	chr4:2815600-2817000	Strong transcription	Fetal Stomach	stomach
42	chr4:2815600-2817200	Enhancers	Duodenum Mucosa	Duodenum
43	chr4:2815600-2817600	Genic enhancers	Skeletal Muscle Male	skeletal muscle
44	chr4:2815600-2818200	Weak transcription	Brain Anterior Caudate	brain
45	chr4:2815600-2818200	Weak transcription	Osteobl	bone
46	chr4:2815600-2818400	Genic enhancers	Primary B cells from peripheral blood	blood
47	chr4:2815600-2818800	Weak transcription	HUVEC	blood vessel
48	chr4:2815600-2819000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr4:2815600-2819000	Weak transcription	Fetal Brain Female	brain
50	chr4:2815600-2819000	Weak transcription	Rectal Mucosa Donor 31	rectum

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