Variant report

Variant	rs28449232
Chromosome Location	chr5:177029234-177029235
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	chr5:177028714-177029850	K562	blood:	n/a	n/a
2	POLR2A	chr5:177028178-177029398	K562	blood:	n/a	n/a
3	GATA3	chr5:177029185-177029533	MCF-7	breast:	n/a	chr5:177029426-177029436 chr5:177029428-177029435 chr5:177029427-177029435 chr5:177029417-177029434 chr5:177029428-177029435 chr5:177029426-177029435 chr5:177029428-177029435
4	POLR2A	chr5:177029097-177029524	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr5:177028523-177029699	HepG2	liver:	n/a	n/a
6	POLR2A	chr5:177026652-177029268	IMR90	lung:	n/a	n/a
7	POLR2A	chr5:177028515-177029414	SK-N-MC	brain:	n/a	n/a
8	POLR2A	chr5:177028300-177029364	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:176829951..176832632-chr5:177027363..177029405,3	K562	blood:
2	chr5:176979030..176982090-chr5:177027612..177030348,3	K562	blood:
3	chr5:177028879..177031069-chr5:177037476..177041584,3	MCF-7	breast:
4	chr5:176942605..176945227-chr5:177026714..177029241,3	K562	blood:
5	chr5:176942493..176944905-chr5:177027413..177029241,2	K562	blood:
6	chr5:176935179..176936864-chr5:177027186..177030051,3	K562	blood:
7	chr5:176935179..176936864-chr5:177027186..177029298,2	K562	blood:
8	chr5:176947981..176948752-chr5:177028732..177029280,2	MCF-7	breast:
9	chr5:176923028..176926285-chr5:177025596..177029619,3	MCF-7	breast:
10	chr5:176979154..176982725-chr5:177026070..177029438,5	MCF-7	breast:

Variant related genes	Relation type
B4GALT7	TF binding region
ENSG00000131187	Chromatin interaction
ENSG00000196923	Chromatin interaction
ENSG00000272459	Chromatin interaction
ENSG00000183258	Chromatin interaction
ENSG00000198055	Chromatin interaction
ENSG00000146094	Chromatin interaction
ENSG00000247679	Chromatin interaction
ENSG00000146067	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs28398967	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28523617	0.80[AFR][1000 genomes]
rs4607363	1.00[EUR][1000 genomes]
rs4976702	1.00[EUR][1000 genomes]
rs6882653	1.00[AFR][1000 genomes]
rs755873	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs901378	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
3	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
4	nsv883181	chr5:176978496-177034786	Bivalent/Poised TSS Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv883182	chr5:176980995-177322056	Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
6	nsv883183	chr5:177019379-177030351	Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:177028000-177029400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:177028000-177029600	Enhancers	Gastric	stomach
3	chr5:177028000-177029800	Enhancers	Esophagus	oesophagus
4	chr5:177028000-177030600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr5:177028000-177032200	Weak transcription	Aorta	Aorta
6	chr5:177028000-177034200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr5:177028000-177034200	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr5:177028000-177040000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr5:177028200-177029400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr5:177028200-177029600	Enhancers	Brain Cingulate Gyrus	brain
11	chr5:177028200-177029800	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr5:177028200-177029800	Enhancers	Adipose Nuclei	Adipose
13	chr5:177028200-177029800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr5:177028200-177031400	Weak transcription	Thymus	Thymus
15	chr5:177028200-177033600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr5:177028200-177034200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr5:177028200-177034400	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr5:177028200-177035600	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr5:177028200-177036400	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr5:177028200-177038000	Weak transcription	Right Atrium	heart
21	chr5:177028400-177029400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr5:177028400-177029800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr5:177028400-177029800	Enhancers	Pancreas	Pancrea
24	chr5:177028400-177030000	Enhancers	Brain Hippocampus Middle	brain
25	chr5:177028400-177030000	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr5:177028400-177030200	Weak transcription	Placenta	Placenta
27	chr5:177028400-177030200	Weak transcription	HSMMtube	muscle
28	chr5:177028400-177030400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr5:177028400-177030400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr5:177028400-177030600	Weak transcription	Spleen	Spleen
31	chr5:177028400-177030800	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr5:177028400-177031200	Weak transcription	Colonic Mucosa	Colon
33	chr5:177028400-177031600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr5:177028400-177031800	Weak transcription	Primary T cells from cord blood	blood
35	chr5:177028400-177031800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr5:177028400-177032000	Weak transcription	Lung	lung
37	chr5:177028400-177032000	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr5:177028400-177032200	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr5:177028400-177034000	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr5:177028400-177034000	Weak transcription	A549	lung
41	chr5:177028400-177034200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr5:177028400-177034200	Weak transcription	Rectal Smooth Muscle	rectum
43	chr5:177028400-177034800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr5:177028400-177036600	Weak transcription	HMEC	breast
45	chr5:177028400-177040200	Weak transcription	Primary hematopoietic stem cells	blood
46	chr5:177028400-177042600	Weak transcription	Primary B cells from cord blood	blood
47	chr5:177028400-177044800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr5:177028400-177045800	Weak transcription	Left Ventricle	heart
49	chr5:177028400-177045800	Weak transcription	Psoas Muscle	Psoas
50	chr5:177028400-177048400	Weak transcription	NH-A	brain

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