Variant report

Variant	rs28587302
Chromosome Location	chr5:176928515-176928516
allele	A/G
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	POU2F2	chr5:176927939-176928679	GM12878	blood:	n/a	n/a
2	STAT5A	chr5:176927755-176929006	GM12878	blood:	n/a	chr5:176928200-176928223
3	POLR2A	chr5:176927842-176931190	GM12892	blood:	n/a	n/a
4	POLR2A	chr5:176927968-176930770	GM18505	blood:	n/a	n/a
5	POLR2A	chr5:176927817-176931184	GM12891	blood:	n/a	n/a
6	POLR2A	chr5:176927942-176928888	Raji	blood:	n/a	n/a
7	MTA3	chr5:176927870-176928764	GM12878	blood:	n/a	n/a
8	CTCF	chr5:176928480-176928630	HA-sp	spinal cord:	n/a	n/a
9	POLR2A	chr5:176927803-176931354	HL-60	blood:	n/a	n/a
10	CTCF	chr5:176928440-176928590	HUVEC	blood vessel:	n/a	n/a
11	CTCF	chr5:176927645-176928643	HCT-116	colon:	n/a	chr5:176928140-176928153 chr5:176928133-176928154 chr5:176928141-176928151 chr5:176928139-176928155 chr5:176928144-176928153 chr5:176928138-176928156 chr5:176928140-176928153
12	CTCF	chr5:176928440-176928590	GM12870	blood:	n/a	n/a
13	POLR2A	chr5:176927729-176928921	GM12891	blood:	n/a	n/a
14	CTCF	chr5:176927988-176928542	GM12878	blood:	n/a	chr5:176928140-176928153 chr5:176928133-176928154 chr5:176928141-176928151 chr5:176928139-176928155 chr5:176928144-176928153 chr5:176928138-176928156 chr5:176928140-176928153
15	POLR2A	chr5:176928374-176928587	HepG2	liver:	n/a	n/a
16	POLR2A	chr5:176927951-176928940	GM15510	blood:	n/a	n/a
17	CTCF	chr5:176927990-176928533	GM12892	blood:	n/a	chr5:176928140-176928153 chr5:176928133-176928154 chr5:176928141-176928151 chr5:176928139-176928155 chr5:176928144-176928153 chr5:176928138-176928156 chr5:176928140-176928153
18	POLR2A	chr5:176927747-176932792	GM12878	blood:	n/a	n/a
19	FOXM1	chr5:176927853-176928556	GM12878	blood:	n/a	n/a
20	EBF1	chr5:176927851-176928644	GM12878	blood:	n/a	chr5:176928074-176928085 chr5:176928075-176928085 chr5:176928076-176928085
21	POLR2A	chr5:176927853-176928786	K562	blood:	n/a	n/a
22	STAT5A	chr5:176927791-176930130	GM12878	blood:	n/a	chr5:176928200-176928223
23	BCL3	chr5:176927979-176929495	GM12878	blood:	n/a	n/a
24	POLR2A	chr5:176927876-176928884	GM12878	blood:	n/a	n/a
25	POLR2A	chr5:176928016-176931000	K562	blood:	n/a	n/a
26	POLR2A	chr5:176928253-176928922	GM12878	blood:	n/a	n/a
27	POLR2A	chr5:176927883-176931090	GM12891	blood:	n/a	n/a
28	NFATC1	chr5:176927788-176929721	GM12878	blood:	n/a	n/a
29	RAD21	chr5:176927931-176928545	GM12878	blood:	n/a	chr5:176928136-176928155 chr5:176928138-176928150 chr5:176928424-176928438 chr5:176928140-176928154 chr5:176928142-176928151 chr5:176928073-176928083
30	CTCF	chr5:176927695-176928639	A549	lung:	n/a	chr5:176928140-176928153 chr5:176928133-176928154 chr5:176928141-176928151 chr5:176928139-176928155 chr5:176928144-176928153 chr5:176928138-176928156 chr5:176928140-176928153
31	MTA3	chr5:176927520-176930398	GM12878	blood:	n/a	n/a
32	CTCF	chr5:176928460-176928610	HVMF	connective:	n/a	n/a
33	SMC3	chr5:176927486-176928782	SK-N-SH	brain:	n/a	chr5:176928147-176928154 chr5:176928191-176928199 chr5:176928140-176928154
34	POLR2A	chr5:176927921-176931030	GM12878	blood:	n/a	n/a
35	ATF2	chr5:176927895-176928619	GM12878	blood:	n/a	n/a
36	RAD21	chr5:176927629-176928572	HCT-116	colon:	n/a	chr5:176928136-176928155 chr5:176928138-176928150 chr5:176928424-176928438 chr5:176928140-176928154 chr5:176928142-176928151 chr5:176928073-176928083
37	POLR2A	chr5:176927942-176928970	K562	blood:	n/a	n/a
38	POLR2A	chr5:176927772-176928885	GM12892	blood:	n/a	n/a
39	PML	chr5:176927703-176930343	GM12878	blood:	n/a	n/a
40	CHD2	chr5:176927979-176930539	GM12878	blood:	n/a	n/a
41	CTCF	chr5:176928342-176928533	GM19240	blood:	n/a	n/a
42	CTCF	chr5:176927976-176928546	GM19238	blood:	n/a	chr5:176928140-176928153 chr5:176928133-176928154 chr5:176928141-176928151 chr5:176928139-176928155 chr5:176928144-176928153 chr5:176928138-176928156 chr5:176928140-176928153
43	POLR2A	chr5:176927838-176932828	HL-60	blood:	n/a	n/a
44	POLR2A	chr5:176928224-176928897	GM12891	blood:	n/a	n/a
45	NFIC	chr5:176927891-176928530	GM12878	blood:	n/a	n/a
46	RUNX3	chr5:176927895-176928783	GM12878	blood:	n/a	n/a
47	REST	chr5:176927583-176928596	H1-neurons	neurons:	n/a	n/a
48	RAD21	chr5:176927475-176928696	SK-N-SH	brain:	n/a	chr5:176928136-176928155 chr5:176928138-176928150 chr5:176928424-176928438 chr5:176928140-176928154 chr5:176928142-176928151 chr5:176928073-176928083
49	POLR2A	chr5:176927930-176928811	Hela-S3	cervix:	n/a	n/a
50	STAT3	chr5:176928433-176928583	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:176914716..176915651-chr5:176927582..176928570,2	MCF-7	breast:
2	chr5:176918064..176919206-chr5:176927577..176928653,10	K562	blood:
3	chr5:176927916..176928713-chr5:176935953..176937217,3	MCF-7	breast:
4	chr3:13461327..13462251-chr5:176928094..176928857,2	MCF-7	breast:
5	chr5:176759238..176761473-chr5:176928139..176930069,2	MCF-7	breast:
6	chr5:176830443..176832059-chr5:176927149..176928539,8	K562	blood:
7	chr5:176831572..176832079-chr5:176927731..176928689,2	MCF-7	breast:
8	chr5:176762919..176763487-chr5:176927677..176928557,2	MCF-7	breast:
9	chr5:176817551..176818141-chr5:176927706..176928668,2	K562	blood:
10	chr5:176926429..176929073-chr5:177031602..177034332,2	K562	blood:
11	chr5:176882418..176883207-chr5:176928109..176928698,2	MCF-7	breast:
12	chr5:176928239..176929895-chr5:177020806..177023092,2	MCF-7	breast:
13	chr5:176814610..176818995-chr5:176923007..176929143,6	MCF-7	breast:
14	chr5:176918128..176919148-chr5:176927678..176928761,5	MCF-7	breast:
15	chr5:176928327..176929846-chr5:177027652..177029155,2	K562	blood:
16	chr5:176731427..176733282-chr5:176928163..176931124,2	MCF-7	breast:

Variant related genes	Relation type
PDLIM7	TF binding region
ENSG00000169230	Chromatin interaction
ENSG00000132182	Chromatin interaction
ENSG00000198055	Chromatin interaction
ENSG00000131183	Chromatin interaction
ENSG00000146094	Chromatin interaction
ENSG00000027847	Chromatin interaction
ENSG00000131187	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs28379386	1.00[AMR][1000 genomes]
rs28392715	1.00[AMR][1000 genomes]
rs28396982	1.00[AMR][1000 genomes]
rs28464438	1.00[AMR][1000 genomes]
rs28483466	1.00[AMR][1000 genomes]
rs28491669	1.00[AMR][1000 genomes]
rs28494836	1.00[AMR][1000 genomes]
rs28613023	1.00[AMR][1000 genomes]
rs28615269	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28688891	1.00[AMR][1000 genomes]
rs28723606	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: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:112 , 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	chr5:176925600-176928600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr5:176925600-176928600	Enhancers	Skeletal Muscle Female	skeletal muscle
7	chr5:176925600-176928800	Enhancers	Skeletal Muscle Male	skeletal muscle
8	chr5:176925600-176929400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr5:176925600-176929600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr5:176925600-176929600	Weak transcription	Esophagus	oesophagus
11	chr5:176925600-176930800	Weak transcription	Lung	lung
12	chr5:176925600-176930800	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr5:176925600-176934400	Weak transcription	Pancreas	Pancrea
14	chr5:176925600-176942400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr5:176925800-176929800	Weak transcription	NHEK	skin
16	chr5:176925800-176930400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr5:176925800-176935200	Weak transcription	Colonic Mucosa	Colon
18	chr5:176925800-176936400	Weak transcription	Psoas Muscle	Psoas
19	chr5:176925800-176937000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr5:176926000-176928600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr5:176926000-176929600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr5:176926000-176937600	Weak transcription	Ovary	ovary
23	chr5:176926600-176928600	Enhancers	HSMM	muscle
24	chr5:176926800-176928800	Enhancers	Fetal Stomach	stomach
25	chr5:176927000-176928800	Enhancers	Fetal Muscle Trunk	muscle
26	chr5:176927000-176928800	Enhancers	NHLF	lung
27	chr5:176927000-176929000	Enhancers	Fetal Muscle Leg	muscle
28	chr5:176927000-176942000	Weak transcription	Fetal Kidney	kidney
29	chr5:176927400-176931000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr5:176927600-176928600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr5:176927600-176928600	Enhancers	Brain Cingulate Gyrus	brain
32	chr5:176927600-176928600	Enhancers	Duodenum Smooth Muscle	Duodenum
33	chr5:176927600-176928600	Enhancers	Fetal Heart	heart
34	chr5:176927600-176928600	Enhancers	Stomach Smooth Muscle	stomach
35	chr5:176927600-176928600	Enhancers	A549	lung
36	chr5:176927600-176928600	Enhancers	Hela-S3	cervix
37	chr5:176927600-176928600	Enhancers	NHDF-Ad	bronchial
38	chr5:176927600-176929600	Enhancers	Primary B cells from peripheral blood	blood
39	chr5:176927600-176929800	Enhancers	Brain Anterior Caudate	brain
40	chr5:176927600-176930400	Enhancers	Primary B cells from cord blood	blood
41	chr5:176927600-176931200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr5:176927800-176928600	Enhancers	H1 Cell Line	embryonic stem cell
43	chr5:176927800-176928600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr5:176927800-176928600	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chr5:176927800-176928600	Enhancers	iPS-15b Cell Line	embryonic stem cell
46	chr5:176927800-176928600	Enhancers	iPS-18 Cell Line	embryonic stem cell
47	chr5:176927800-176928600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr5:176927800-176928600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
49	chr5:176927800-176928600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr5:176927800-176928600	Enhancers	Fetal Thymus	thymus

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