Variant report

Variant	rs28565502
Chromosome Location	chr5:176936650-176936651
allele	C/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	ELF1	chr5:176936394-176936812	K562	blood:	n/a	n/a
2	ZNF143	chr5:176936556-176936949	GM12878	blood:	n/a	chr5:176936909-176936927
3	NRF1	chr5:176936646-176937093	GM12878	blood:	n/a	n/a
4	SPI1	chr5:176936400-176936803	GM12878	blood:	n/a	n/a
5	TCF12	chr5:176936457-176937017	GM12878	blood:	n/a	n/a
6	FOXM1	chr5:176936379-176937996	GM12878	blood:	n/a	n/a
7	TAF1	chr5:176936627-176936968	GM12878	blood:	n/a	n/a
8	YY1	chr5:176936387-176936757	K562	blood:	n/a	chr5:176936696-176936707 chr5:176936669-176936680
9	CTCF	chr5:176936460-176936657	K562	blood:	n/a	n/a
10	POLR2A	chr5:176936449-176937332	K562	blood:	n/a	n/a
11	CHD2	chr5:176935359-176938196	GM12878	blood:	n/a	chr5:176937490-176937497 chr5:176936668-176936678
12	POLR2A	chr5:176933894-176938451	GM12878	blood:	n/a	n/a
13	YY1	chr5:176936506-176936680	K562	blood:	n/a	chr5:176936669-176936680
14	ELF1	chr5:176934745-176938039	GM12878	blood:	n/a	n/a
15	SPI1	chr5:176936366-176936848	HL-60	blood:	n/a	n/a
16	ZMIZ1	chr5:176936569-176936794	K562	blood:	n/a	n/a
17	PML	chr5:176935473-176938644	GM12878	blood:	n/a	chr5:176938357-176938366
18	POLR2A	chr5:176934786-176938541	GM19193	blood:	n/a	n/a
19	SPI1	chr5:176936387-176936797	GM12891	blood:	n/a	n/a
20	TEAD4	chr5:176936411-176937013	K562	blood:	n/a	n/a
21	POLR2A	chr5:176936633-176936938	ECC-1	luminal epithelium:	n/a	n/a
22	MAX	chr5:176936538-176936995	K562	blood:	n/a	chr5:176936662-176936672
23	EP300	chr5:176936576-176936696	GM12878	blood:	n/a	n/a
24	HCFC1	chr5:176936457-176936870	K562	blood:	n/a	n/a
25	CHD2	chr5:176936371-176936923	K562	blood:	n/a	chr5:176936668-176936678
26	ELF1	chr5:176936422-176936846	K562	blood:	n/a	n/a
27	POLR2A	chr5:176934713-176942234	K562	blood:	n/a	n/a
28	POLR2A	chr5:176935986-176938601	U87	brain:	n/a	n/a
29	TBL1XR1	chr5:176935027-176937953	GM12878	blood:	n/a	n/a
30	UBTF	chr5:176936496-176936916	K562	blood:	n/a	n/a
31	RCOR1	chr5:176936386-176936858	GM12878	blood:	n/a	n/a
32	MAX	chr5:176936407-176938173	NB4	blood:	n/a	chr5:176937409-176937420 chr5:176937375-176937385 chr5:176937409-176937420 chr5:176937409-176937418 chr5:176936662-176936672
33	POLR2A	chr5:176936177-176936821	PANC-1	pancreas:	n/a	n/a
34	MAX	chr5:176936497-176936984	K562	blood:	n/a	chr5:176936662-176936672
35	POLR2A	chr5:176934161-176938395	GM12892	blood:	n/a	n/a
36	TCF3	chr5:176936413-176937097	GM12878	blood:	n/a	n/a
37	POLR2A	chr5:176936397-176936936	Hela-S3	cervix:	n/a	n/a
38	EBF1	chr5:176936292-176938584	GM12878	blood:	n/a	chr5:176936721-176936730 chr5:176937432-176937443
39	EP300	chr5:176936453-176936804	K562	blood:	n/a	n/a
40	MAX	chr5:176935475-176938147	GM12878	blood:	n/a	chr5:176937409-176937420 chr5:176937375-176937385 chr5:176937409-176937420 chr5:176937409-176937418 chr5:176936662-176936672
41	SPI1	chr5:176936468-176936775	K562	blood:	n/a	n/a
42	STAT5A	chr5:176934168-176938267	GM12878	blood:	n/a	chr5:176937939-176937947 chr5:176936908-176936920 chr5:176936717-176936725
43	POLR2A	chr5:176935852-176938145	NB4	blood:	n/a	n/a
44	PAX5	chr5:176936459-176937522	GM12878	blood:	n/a	n/a
45	POLR2A	chr5:176935992-176938515	U87	brain:	n/a	n/a
46	POLR2A	chr5:176935647-176938196	GM12892	blood:	n/a	n/a
47	POLR2A	chr5:176934801-176938447	GM15510	blood:	n/a	n/a
48	ELF1	chr5:176935575-176936937	GM12878	blood:	n/a	n/a
49	POLR2A	chr5:176935792-176937201	HepG2	liver:	n/a	n/a
50	BHLHE40	chr5:176935860-176937463	K562	blood:	n/a	chr5:176936878-176936894 chr5:176936875-176936891

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:176935179..176936864-chr5:177027186..177030051,3	K562	blood:
2	chr5:176935179..176936864-chr5:177027186..177029298,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DDX41-1	chr5:176935785-176936658	NONHSAT105428
2	lnc-DDX41-1	chr5:176936167-176936658	NONHSAT105429

Variant related genes	Relation type
DOK3	TF binding region
ENSG00000027847	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs28464438	0.84[AFR][1000 genomes]
rs28483466	0.84[AFR][1000 genomes]
rs28491669	0.84[AFR][1000 genomes]
rs28494836	0.84[AFR][1000 genomes]
rs28613023	0.84[AFR][1000 genomes]
rs28688891	0.84[AFR][1000 genomes]
rs28723606	0.84[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 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	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	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:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:176925400-176937200	Weak transcription	Aorta	Aorta
2	chr5:176925400-176937200	Weak transcription	Dnd41	blood
3	chr5:176925600-176942400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr5:176925800-176937000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr5:176926000-176937600	Weak transcription	Ovary	ovary
6	chr5:176927000-176942000	Weak transcription	Fetal Kidney	kidney
7	chr5:176928000-176937000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr5:176928000-176937400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr5:176928000-176937400	Weak transcription	Osteobl	bone
10	chr5:176928000-176937600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr5:176928000-176937600	Weak transcription	Primary T cells from cord blood	blood
12	chr5:176928000-176938200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr5:176928200-176937400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr5:176928200-176937400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr5:176928200-176937600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr5:176928400-176937000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr5:176928400-176937600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr5:176928400-176937600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr5:176928400-176937600	Weak transcription	Brain Angular Gyrus	brain
20	chr5:176928400-176937600	Weak transcription	Colon Smooth Muscle	Colon
21	chr5:176928400-176937600	Weak transcription	NH-A	brain
22	chr5:176928400-176938200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr5:176928400-176941000	Weak transcription	Fetal Brain Male	brain
24	chr5:176928600-176937000	Weak transcription	A549	lung
25	chr5:176928600-176937400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr5:176928600-176937400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr5:176928600-176937600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr5:176928600-176937600	Weak transcription	Hela-S3	cervix
29	chr5:176928600-176939600	Weak transcription	NHDF-Ad	bronchial
30	chr5:176928800-176938200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr5:176930600-176937600	Weak transcription	HMEC	breast
32	chr5:176930600-176942400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr5:176931000-176937600	Weak transcription	HepG2	liver
34	chr5:176932000-176937400	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr5:176932000-176937800	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr5:176934000-176942600	Strong transcription	Fetal Intestine Small	intestine
37	chr5:176934200-176937200	Active TSS	Rectal Mucosa Donor 29	rectum
38	chr5:176934200-176941800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr5:176934400-176937200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr5:176934400-176937600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr5:176934400-176937600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr5:176934400-176938200	Flanking Active TSS	Primary B cells from cord blood	blood
43	chr5:176934400-176941000	Strong transcription	Brain Germinal Matrix	brain
44	chr5:176934600-176937400	Flanking Active TSS	Primary hematopoietic stem cells	blood
45	chr5:176934600-176937400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
46	chr5:176934600-176941600	Strong transcription	Fetal Stomach	stomach
47	chr5:176934800-176936800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr5:176934800-176937000	Active TSS	Duodenum Smooth Muscle	Duodenum
49	chr5:176934800-176937400	Active TSS	Rectal Smooth Muscle	rectum
50	chr5:176934800-176937800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin

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