Variant report

Variant	rs2560844
Chromosome Location	chr5:16902229-16902230
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	chr5:16899974..16902321-chr5:16904564..16907062,3	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs253483	0.85[ASN][1000 genomes]
rs253484	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2560842	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2560843	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2560846	0.86[ASN][1000 genomes]
rs2560848	0.85[ASN][1000 genomes]
rs2562350	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2562352	0.81[ASN][1000 genomes]
rs2562353	0.85[ASN][1000 genomes]
rs2562354	0.85[ASN][1000 genomes]
rs2562356	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2562357	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2562358	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2625172	0.82[ASN][1000 genomes]
rs2625173	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2625174	0.86[ASN][1000 genomes]
rs2625175	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025225	chr5:16714512-17234866	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1015247	chr5:16748966-17133274	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	esv2762500	chr5:16815489-16952565	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
4	nsv880277	chr5:16829442-17316288	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv1034844	chr5:16854341-16903100	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	esv3485757	chr5:16856475-16966851	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
7	esv3485758	chr5:16856475-16966851	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
8	nsv968877	chr5:16901612-16905258	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:16895000-16903000	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr5:16896000-16912400	Weak transcription	Esophagus	oesophagus
3	chr5:16897000-16902800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr5:16898000-16902800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr5:16898000-16902800	Weak transcription	HSMM	muscle
6	chr5:16898200-16902600	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr5:16898200-16902800	Weak transcription	Colon Smooth Muscle	Colon
8	chr5:16898200-16903000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr5:16898200-16903400	Weak transcription	Placenta	Placenta
10	chr5:16898200-16903800	Weak transcription	Osteobl	bone
11	chr5:16898200-16904000	Weak transcription	NHLF	lung
12	chr5:16898200-16906200	Weak transcription	Psoas Muscle	Psoas
13	chr5:16898200-16912600	Weak transcription	NH-A	brain
14	chr5:16898400-16903000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr5:16898400-16903000	Weak transcription	Fetal Stomach	stomach
16	chr5:16898400-16903000	Weak transcription	Ovary	ovary
17	chr5:16898400-16903800	Weak transcription	Small Intestine	intestine
18	chr5:16898400-16904600	Weak transcription	Fetal Intestine Small	intestine
19	chr5:16899400-16907000	Enhancers	Pancreas	Pancrea
20	chr5:16899800-16905600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr5:16899800-16910000	Weak transcription	HUVEC	blood vessel
22	chr5:16899800-16910800	Weak transcription	HMEC	breast
23	chr5:16900400-16905400	Enhancers	Fetal Muscle Leg	muscle
24	chr5:16900600-16903800	Weak transcription	NHDF-Ad	bronchial
25	chr5:16900600-16903800	Weak transcription	NHEK	skin
26	chr5:16900800-16903200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr5:16900800-16903200	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr5:16901200-16902400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr5:16901200-16904400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr5:16901200-16904800	Enhancers	Fetal Muscle Trunk	muscle
31	chr5:16901200-16906400	Enhancers	Gastric	stomach
32	chr5:16901200-16907000	Enhancers	Lung	lung
33	chr5:16901400-16903800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr5:16901400-16906400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr5:16901400-16907600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr5:16901600-16903000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr5:16901600-16903000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr5:16901600-16903000	Weak transcription	Fetal Lung	lung
39	chr5:16901600-16905200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr5:16901600-16906000	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr5:16901600-16907600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr5:16901600-16909400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr5:16901800-16902600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr5:16901800-16902800	Weak transcription	Stomach Mucosa	stomach
45	chr5:16902000-16902400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr5:16902000-16902400	Weak transcription	HSMMtube	muscle
47	chr5:16902000-16903200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr5:16902000-16903600	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr5:16902000-16903600	Weak transcription	Duodenum Mucosa	Duodenum
50	chr5:16902000-16903800	Enhancers	A549	lung

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