Variant report

Variant	rs28613023
Chromosome Location	chr5:176937308-176937309
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	POLR2A	chr5:176937032-176937379	Hela-S3	cervix:	n/a	n/a
2	EGR1	chr5:176937297-176937598	K562	blood:	n/a	chr5:176937417-176937431
3	FOXM1	chr5:176936379-176937996	GM12878	blood:	n/a	n/a
4	POU2F2	chr5:176937078-176938258	GM12891	blood:	n/a	n/a
5	POLR2A	chr5:176936449-176937332	K562	blood:	n/a	n/a
6	NFE2	chr5:176937279-176937581	GM12878	blood:	n/a	n/a
7	CHD2	chr5:176935359-176938196	GM12878	blood:	n/a	chr5:176937490-176937497 chr5:176936668-176936678
8	ATF2	chr5:176937122-176937820	GM12878	blood:	n/a	n/a
9	EP300	chr5:176937221-176937546	GM12878	blood:	n/a	n/a
10	POLR2A	chr5:176933894-176938451	GM12878	blood:	n/a	n/a
11	WRNIP1	chr5:176937113-176938070	GM12878	blood:	n/a	n/a
12	PML	chr5:176937242-176937442	GM12878	blood:	n/a	n/a
13	ELF1	chr5:176934745-176938039	GM12878	blood:	n/a	n/a
14	PML	chr5:176935473-176938644	GM12878	blood:	n/a	chr5:176938357-176938366
15	REST	chr5:176937209-176938215	HL-60	blood:	n/a	chr5:176938187-176938200
16	POLR2A	chr5:176934786-176938541	GM19193	blood:	n/a	n/a
17	EGR1	chr5:176937263-176937517	GM12878	blood:	n/a	chr5:176937417-176937431
18	POLR2A	chr5:176937225-176938724	HepG2	liver:	n/a	n/a
19	MYC	chr5:176937282-176937522	K562	blood:	n/a	chr5:176937409-176937420 chr5:176937375-176937385 chr5:176937409-176937420 chr5:176937409-176937418
20	POLR2A	chr5:176934713-176942234	K562	blood:	n/a	n/a
21	MYC	chr5:176937206-176937482	GM12878	blood:	n/a	chr5:176937409-176937420 chr5:176937375-176937385 chr5:176937409-176937420 chr5:176937409-176937418
22	POLR2A	chr5:176935986-176938601	U87	brain:	n/a	n/a
23	USF1	chr5:176937224-176937575	GM12878	blood:	n/a	n/a
24	TBL1XR1	chr5:176935027-176937953	GM12878	blood:	n/a	n/a
25	MAX	chr5:176936407-176938173	NB4	blood:	n/a	chr5:176937409-176937420 chr5:176937375-176937385 chr5:176937409-176937420 chr5:176937409-176937418 chr5:176936662-176936672
26	USF1	chr5:176937140-176937610	K562	blood:	n/a	n/a
27	POLR2A	chr5:176934161-176938395	GM12892	blood:	n/a	n/a
28	NFATC1	chr5:176937177-176937929	GM12878	blood:	n/a	n/a
29	EBF1	chr5:176936292-176938584	GM12878	blood:	n/a	chr5:176936721-176936730 chr5:176937432-176937443
30	POLR2A	chr5:176937123-176937340	HCT-116	colon:	n/a	n/a
31	YY1	chr5:176937213-176938063	GM12878	blood:	n/a	n/a
32	MAX	chr5:176935475-176938147	GM12878	blood:	n/a	chr5:176937409-176937420 chr5:176937375-176937385 chr5:176937409-176937420 chr5:176937409-176937418 chr5:176936662-176936672
33	RFX5	chr5:176937285-176937570	GM12878	blood:	n/a	n/a
34	POLR2A	chr5:176937101-176937381	H1-hESC	embryonic stem cell:	n/a	n/a
35	STAT5A	chr5:176934168-176938267	GM12878	blood:	n/a	chr5:176937939-176937947 chr5:176936908-176936920 chr5:176936717-176936725
36	POLR2A	chr5:176935852-176938145	NB4	blood:	n/a	n/a
37	PAX5	chr5:176936459-176937522	GM12878	blood:	n/a	n/a
38	POLR2A	chr5:176935992-176938515	U87	brain:	n/a	n/a
39	POLR2A	chr5:176935647-176938196	GM12892	blood:	n/a	n/a
40	POLR2A	chr5:176934801-176938447	GM15510	blood:	n/a	n/a
41	MAX	chr5:176937210-176937559	K562	blood:	n/a	chr5:176937409-176937420 chr5:176937375-176937385 chr5:176937409-176937420 chr5:176937409-176937418
42	ZNF143	chr5:176937276-176937980	GM12878	blood:	n/a	n/a
43	POLR2A	chr5:176937189-176937387	A549	lung:	n/a	n/a
44	MAX	chr5:176937154-176937602	K562	blood:	n/a	chr5:176937409-176937420 chr5:176937375-176937385 chr5:176937409-176937420 chr5:176937409-176937418
45	BHLHE40	chr5:176935860-176937463	K562	blood:	n/a	chr5:176936878-176936894 chr5:176936875-176936891
46	POLR2A	chr5:176935217-176938145	GM12878	blood:	n/a	n/a
47	MTA3	chr5:176934175-176938400	GM12878	blood:	n/a	n/a
48	POLR2A	chr5:176937131-176938095	GM12891	blood:	n/a	n/a
49	POLR2A	chr5:176936596-176937359	PFSK-1	brain:	n/a	n/a
50	POLR2A	chr5:176935747-176938115	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:176936816..176938708-chr5:177019651..177022498,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DDX41-1	chr5:176937261-176937383	NONHSAT105428

Variant related genes	Relation type
DOK3	TF binding region
ENSG00000184840	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs28379386	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28392715	1.00[AMR][1000 genomes]
rs28396982	1.00[AMR][1000 genomes]
rs28464438	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28483466	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28491669	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28494836	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28565502	0.84[AFR][1000 genomes]
rs28587302	1.00[AMR][1000 genomes]
rs28615269	1.00[AMR][1000 genomes]
rs28630512	0.94[AFR][1000 genomes]
rs28688891	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28723606	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs337387	1.00[AMR][1000 genomes]
rs337399	1.00[AMR][1000 genomes]
rs388783	1.00[AMR][1000 genomes]
rs4976650	1.00[AMR][1000 genomes]
rs5013573	1.00[AMR][1000 genomes]
rs58021881	1.00[AMR][1000 genomes]
rs6600953	1.00[AMR][1000 genomes]
rs7444245	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 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	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	chr5:176925600-176942400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr5:176926000-176937600	Weak transcription	Ovary	ovary
3	chr5:176927000-176942000	Weak transcription	Fetal Kidney	kidney
4	chr5:176928000-176937400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr5:176928000-176937400	Weak transcription	Osteobl	bone
6	chr5:176928000-176937600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr5:176928000-176937600	Weak transcription	Primary T cells from cord blood	blood
8	chr5:176928000-176938200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr5:176928200-176937400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr5:176928200-176937400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr5:176928200-176937600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr5:176928400-176937600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr5:176928400-176937600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr5:176928400-176937600	Weak transcription	Brain Angular Gyrus	brain
15	chr5:176928400-176937600	Weak transcription	Colon Smooth Muscle	Colon
16	chr5:176928400-176937600	Weak transcription	NH-A	brain
17	chr5:176928400-176938200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr5:176928400-176941000	Weak transcription	Fetal Brain Male	brain
19	chr5:176928600-176937400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr5:176928600-176937400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr5:176928600-176937600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr5:176928600-176937600	Weak transcription	Hela-S3	cervix
23	chr5:176928600-176939600	Weak transcription	NHDF-Ad	bronchial
24	chr5:176928800-176938200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr5:176930600-176937600	Weak transcription	HMEC	breast
26	chr5:176930600-176942400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr5:176931000-176937600	Weak transcription	HepG2	liver
28	chr5:176932000-176937400	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr5:176932000-176937800	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr5:176934000-176942600	Strong transcription	Fetal Intestine Small	intestine
31	chr5:176934200-176941800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr5:176934400-176937600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr5:176934400-176937600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr5:176934400-176938200	Flanking Active TSS	Primary B cells from cord blood	blood
35	chr5:176934400-176941000	Strong transcription	Brain Germinal Matrix	brain
36	chr5:176934600-176937400	Flanking Active TSS	Primary hematopoietic stem cells	blood
37	chr5:176934600-176937400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
38	chr5:176934600-176941600	Strong transcription	Fetal Stomach	stomach
39	chr5:176934800-176937400	Active TSS	Rectal Smooth Muscle	rectum
40	chr5:176934800-176937800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr5:176934800-176941800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr5:176935000-176938200	Flanking Active TSS	GM12878-XiMat	blood
43	chr5:176935000-176938600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr5:176935000-176942000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr5:176935200-176937400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
46	chr5:176935200-176937800	Flanking Active TSS	Primary B cells from peripheral blood	blood
47	chr5:176935200-176942400	Strong transcription	Fetal Brain Female	brain
48	chr5:176935200-176942600	Strong transcription	NHLF	lung
49	chr5:176935400-176942000	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr5:176935800-176937400	Enhancers	Primary T cells fromperipheralblood	blood

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