Variant report

Variant	rs28544104
Chromosome Location	chr2:54350353-54350354
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54341216..54345253-chr2:54347980..54351307,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170634	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs13384747	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13395143	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13420388	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13427038	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17045642	1.00[EUR][1000 genomes]
rs28376974	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28445376	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28481646	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28559613	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28599574	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60599526	1.00[EUR][1000 genomes]
rs6720696	1.00[EUR][1000 genomes]
rs6732202	1.00[EUR][1000 genomes]
rs6735998	1.00[EUR][1000 genomes]
rs6757372	1.00[EUR][1000 genomes]
rs7355466	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7355609	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7355635	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7355636	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7355768	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73935091	1.00[EUR][1000 genomes]
rs73935095	1.00[EUR][1000 genomes]
rs73935096	1.00[EUR][1000 genomes]
rs73938020	1.00[EUR][1000 genomes]
rs7558041	1.00[EUR][1000 genomes]
rs7560496	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7593099	1.00[EUR][1000 genomes]
rs7593450	1.00[EUR][1000 genomes]
rs9808489	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9973583	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001246	chr2:54195654-54434832	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
2	nsv1003205	chr2:54220049-54700843	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	esv2762639	chr2:54220049-54700855	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1011790	chr2:54220049-54714553	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv1002891	chr2:54227005-54682169	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv535722	chr2:54227005-54682169	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv1011690	chr2:54255361-54700843	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
8	nsv431069	chr2:54260132-54434049	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	esv1851003	chr2:54324701-54372931	Genic enhancers Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
10	nsv1007731	chr2:54331179-54452329	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
11	nsv535723	chr2:54331179-54452329	Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
12	nsv961690	chr2:54339295-54359290	Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
13	nsv1006984	chr2:54343466-54384094	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
14	nsv874148	chr2:54344325-54432222	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
15	nsv1000652	chr2:54345892-54469703	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
16	nsv1003889	chr2:54347750-54424601	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
17	nsv582011	chr2:54348704-54384927	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54343200-54350600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:54343400-54351000	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr2:54343400-54353000	Weak transcription	Fetal Lung	lung
4	chr2:54343400-54388600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr2:54343600-54350600	Weak transcription	Brain Cingulate Gyrus	brain
6	chr2:54343800-54355800	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr2:54348200-54353600	Weak transcription	Brain Substantia Nigra	brain
8	chr2:54348400-54350400	Weak transcription	Right Atrium	heart
9	chr2:54348400-54351200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr2:54348400-54361800	Weak transcription	Brain Anterior Caudate	brain
11	chr2:54348600-54350800	Weak transcription	Right Ventricle	heart
12	chr2:54348600-54362200	Weak transcription	Liver	Liver
13	chr2:54348600-54365800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr2:54348600-54365800	Weak transcription	Left Ventricle	heart
15	chr2:54348800-54350400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr2:54348800-54350400	Flanking Active TSS	HepG2	liver
17	chr2:54348800-54362000	Weak transcription	Brain Hippocampus Middle	brain
18	chr2:54349000-54352400	Enhancers	NHEK	skin
19	chr2:54349000-54352600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr2:54349200-54366000	Weak transcription	Primary B cells from peripheral blood	blood
21	chr2:54349400-54350600	Enhancers	K562	blood
22	chr2:54349400-54350800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr2:54349400-54350800	Enhancers	NHLF	lung
24	chr2:54349400-54350800	Flanking Active TSS	Osteobl	bone
25	chr2:54349400-54351000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr2:54349400-54351000	Enhancers	Fetal Heart	heart
27	chr2:54349400-54360200	Weak transcription	Primary B cells from cord blood	blood
28	chr2:54349600-54350400	Enhancers	A549	lung
29	chr2:54349600-54350800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr2:54349600-54350800	Enhancers	Placenta Amnion	Placenta Amnion
31	chr2:54349800-54350400	Strong transcription	Primary T cells from cord blood	blood
32	chr2:54349800-54350400	Enhancers	Hela-S3	cervix
33	chr2:54349800-54350800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr2:54349800-54350800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr2:54349800-54350800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr2:54349800-54351000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr2:54349800-54351000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
38	chr2:54349800-54351200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr2:54350000-54350600	Enhancers	Aorta	Aorta
40	chr2:54350000-54350800	Enhancers	Adipose Nuclei	Adipose
41	chr2:54350000-54350800	Flanking Active TSS	NHDF-Ad	bronchial
42	chr2:54350000-54351000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr2:54350000-54351000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
44	chr2:54350000-54351000	Flanking Active TSS	HMEC	breast
45	chr2:54350000-54351000	Flanking Active TSS	HSMM	muscle
46	chr2:54350000-54365800	Weak transcription	Psoas Muscle	Psoas
47	chr2:54350200-54350400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr2:54350200-54350400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr2:54350200-54350400	Weak transcription	Stomach Smooth Muscle	stomach
50	chr2:54350200-54350400	Active TSS	HSMMtube	muscle

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