Variant report

Variant	rs28712799
Chromosome Location	chr5:176929582-176929583
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:50)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:176929255-176929992	K562	blood:	n/a	n/a
2	POLR2A	chr5:176927842-176931190	GM12892	blood:	n/a	n/a
3	POLR2A	chr5:176927968-176930770	GM18505	blood:	n/a	n/a
4	BCLAF1	chr5:176928880-176929762	GM12878	blood:	n/a	n/a
5	POLR2A	chr5:176927817-176931184	GM12891	blood:	n/a	n/a
6	POLR2A	chr5:176927803-176931354	HL-60	blood:	n/a	n/a
7	POLR2A	chr5:176929329-176932771	K562	blood:	n/a	n/a
8	POLR2A	chr5:176929277-176931486	GM15510	blood:	n/a	n/a
9	BCLAF1	chr5:176928907-176929800	GM12878	blood:	n/a	n/a
10	MTA3	chr5:176928898-176929645	GM12878	blood:	n/a	n/a
11	POLR2A	chr5:176927747-176932792	GM12878	blood:	n/a	n/a
12	POLR2A	chr5:176929484-176929737	HepG2	liver:	n/a	n/a
13	STAT5A	chr5:176927791-176930130	GM12878	blood:	n/a	chr5:176928200-176928223
14	POLR2A	chr5:176928016-176931000	K562	blood:	n/a	n/a
15	POLR2A	chr5:176927883-176931090	GM12891	blood:	n/a	n/a
16	NFATC1	chr5:176927788-176929721	GM12878	blood:	n/a	n/a
17	BHLHE40	chr5:176928975-176929593	GM12878	blood:	n/a	n/a
18	POLR2A	chr5:176929085-176930640	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr5:176928995-176930809	GM12878	blood:	n/a	n/a
20	MTA3	chr5:176927520-176930398	GM12878	blood:	n/a	n/a
21	RUNX3	chr5:176928775-176929585	GM12878	blood:	n/a	n/a
22	POLR2A	chr5:176927921-176931030	GM12878	blood:	n/a	n/a
23	ELF1	chr5:176929085-176929658	GM12878	blood:	n/a	n/a
24	MXI1	chr5:176928990-176929649	GM12878	blood:	n/a	n/a
25	POLR2A	chr5:176928946-176931325	GM12891	blood:	n/a	n/a
26	ELF1	chr5:176929558-176930107	GM12878	blood:	n/a	n/a
27	RCOR1	chr5:176929038-176929744	GM12878	blood:	n/a	n/a
28	POLR2A	chr5:176929267-176932713	GM12878	blood:	n/a	n/a
29	PML	chr5:176927703-176930343	GM12878	blood:	n/a	n/a
30	POLR2A	chr5:176929313-176931008	GM19193	blood:	n/a	n/a
31	CHD2	chr5:176927979-176930539	GM12878	blood:	n/a	n/a
32	POLR2A	chr5:176929122-176930258	PBDE	blood:	n/a	n/a
33	POLR2A	chr5:176927838-176932828	HL-60	blood:	n/a	n/a
34	POLR2A	chr5:176929556-176930348	GM12878	blood:	n/a	n/a
35	WRNIP1	chr5:176928728-176929594	GM12878	blood:	n/a	n/a
36	SPI1	chr5:176928796-176929710	GM12878	blood:	n/a	n/a
37	USF2	chr5:176929579-176929776	Hela-S3	cervix:	n/a	n/a
38	POLR2A	chr5:176927468-176932764	GM12878	blood:	n/a	n/a
39	TBL1XR1	chr5:176928532-176929590	GM12878	blood:	n/a	n/a
40	IKZF1	chr5:176928935-176929681	GM12878	blood:	n/a	n/a
41	POLR2A	chr5:176927831-176931240	GM12892	blood:	n/a	n/a
42	USF2	chr5:176928919-176929765	GM12878	blood:	n/a	n/a
43	POLR2A	chr5:176928994-176929777	GM12892	blood:	n/a	n/a
44	POLR2A	chr5:176929513-176929761	GM12891	blood:	n/a	n/a
45	POLR2A	chr5:176927888-176931091	GM12892	blood:	n/a	n/a
46	POLR2A	chr5:176927526-176930861	GM12891	blood:	n/a	n/a
47	ATF2	chr5:176928844-176929633	GM12878	blood:	n/a	n/a
48	ATF2	chr5:176928855-176929817	GM12878	blood:	n/a	n/a
49	PAX5	chr5:176928899-176929592	GM12878	blood:	n/a	n/a
50	RUNX3	chr5:176928911-176929947	GM12878	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:176759238..176761473-chr5:176928139..176930069,2	MCF-7	breast:
2	chr5:176928239..176929895-chr5:177020806..177023092,2	MCF-7	breast:
3	chr5:176928327..176929846-chr5:177027652..177029155,2	K562	blood:
4	chr5:176731427..176733282-chr5:176928163..176931124,2	MCF-7	breast:

No data

Variant related genes	Relation type
PDLIM7	TF binding region
ENSG00000169230	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs1422268	0.95[ASN][1000 genomes]
rs2279398	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2306764	0.85[ASN][1000 genomes]
rs734825	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916108	chr5:176688459-177078723	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
2	nsv883158	chr5:176726635-176931706	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	120 gene(s)	inside rSNPs	diseases
3	nsv883160	chr5:176740996-176952919	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
4	nsv1024444	chr5:176751921-177427715	Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	142 gene(s)	inside rSNPs	diseases
5	nsv883161	chr5:176754722-176958397	Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Genic enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
6	nsv1020334	chr5:176779108-176954933	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
7	nsv883164	chr5:176780545-177003616	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
8	esv1816147	chr5:176787037-176966509	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
9	nsv883166	chr5:176817636-176940384	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
10	nsv883170	chr5:176824137-176952919	Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
11	nsv883173	chr5:176842474-176931706	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
12	nsv883174	chr5:176842474-176940384	Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
13	nsv883175	chr5:176842474-176952919	Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
14	nsv1030965	chr5:176851182-176937654	Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
15	nsv1026103	chr5:176851182-176942552	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
16	nsv1022832	chr5:176861503-176937654	Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer 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 target site	79 gene(s)	inside rSNPs	diseases
17	nsv1018088	chr5:176861503-176942552	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
18	nsv1028123	chr5:176861503-176949149	Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
19	nsv537965	chr5:176861503-176949149	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
20	nsv883177	chr5:176868358-177003616	Genic enhancers Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS 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	84 gene(s)	inside rSNPs	diseases
21	esv2752795	chr5:176898619-177488281	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
22	nsv883180	chr5:176912073-176937177	Genic enhancers Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
23	nsv984570	chr5:176923414-176956300	Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:176925400-176930000	Weak transcription	Gastric	stomach
2	chr5:176925400-176930600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr5:176925400-176937200	Weak transcription	Aorta	Aorta
4	chr5:176925400-176937200	Weak transcription	Dnd41	blood
5	chr5:176925600-176929600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr5:176925600-176929600	Weak transcription	Esophagus	oesophagus
7	chr5:176925600-176930800	Weak transcription	Lung	lung
8	chr5:176925600-176930800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr5:176925600-176934400	Weak transcription	Pancreas	Pancrea
10	chr5:176925600-176942400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr5:176925800-176929800	Weak transcription	NHEK	skin
12	chr5:176925800-176930400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr5:176925800-176935200	Weak transcription	Colonic Mucosa	Colon
14	chr5:176925800-176936400	Weak transcription	Psoas Muscle	Psoas
15	chr5:176925800-176937000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr5:176926000-176929600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr5:176926000-176937600	Weak transcription	Ovary	ovary
18	chr5:176927000-176942000	Weak transcription	Fetal Kidney	kidney
19	chr5:176927400-176931000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr5:176927600-176929600	Enhancers	Primary B cells from peripheral blood	blood
21	chr5:176927600-176929800	Enhancers	Brain Anterior Caudate	brain
22	chr5:176927600-176930400	Enhancers	Primary B cells from cord blood	blood
23	chr5:176927600-176931200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr5:176927800-176929600	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr5:176927800-176930000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
26	chr5:176927800-176930000	Enhancers	Duodenum Mucosa	Duodenum
27	chr5:176927800-176930600	Enhancers	HMEC	breast
28	chr5:176927800-176934800	Weak transcription	Rectal Smooth Muscle	rectum
29	chr5:176928000-176929800	Weak transcription	HSMMtube	muscle
30	chr5:176928000-176930000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr5:176928000-176930000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr5:176928000-176930400	Weak transcription	Fetal Brain Female	brain
33	chr5:176928000-176936000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr5:176928000-176937000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr5:176928000-176937400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr5:176928000-176937400	Weak transcription	Osteobl	bone
37	chr5:176928000-176937600	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr5:176928000-176937600	Weak transcription	Primary T cells from cord blood	blood
39	chr5:176928000-176938200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr5:176928200-176929600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr5:176928200-176930800	Weak transcription	Liver	Liver
42	chr5:176928200-176931000	Weak transcription	Thymus	Thymus
43	chr5:176928200-176931200	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr5:176928200-176931600	Weak transcription	Adipose Nuclei	Adipose
45	chr5:176928200-176936400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr5:176928200-176937400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr5:176928200-176937400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr5:176928200-176937600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr5:176928400-176929600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr5:176928400-176929800	Genic enhancers	Primary neutrophils fromperipheralblood	blood

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