Variant report

Variant	rs29448
Chromosome Location	chr5:16907538-16907539
allele	A/C
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	chr5:16907509-16907680	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:16901561..16905070-chr5:16906190..16907991,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000243538	TF binding region
ENSG00000243538	Chromatin interaction

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

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

rs_ID	r²[population]
rs194135	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs29447	0.93[CHB][hapmap]
rs29449	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs29450	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs29454	0.95[CEU][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs31454	0.94[MEX][hapmap]
rs40983	0.90[AMR][1000 genomes];0.80[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	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	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
6	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

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:16896000-16912400	Weak transcription	Esophagus	oesophagus
2	chr5:16898200-16912600	Weak transcription	NH-A	brain
3	chr5:16899800-16910000	Weak transcription	HUVEC	blood vessel
4	chr5:16899800-16910800	Weak transcription	HMEC	breast
5	chr5:16901400-16907600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr5:16901600-16907600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr5:16901600-16909400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr5:16902000-16912800	Weak transcription	Fetal Intestine Large	intestine
9	chr5:16902200-16913800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr5:16902200-16919000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr5:16902200-16930000	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr5:16904400-16912400	Weak transcription	NHDF-Ad	bronchial
13	chr5:16904400-16912400	Weak transcription	NHLF	lung
14	chr5:16904400-16912400	Weak transcription	Osteobl	bone
15	chr5:16904400-16933200	Weak transcription	Fetal Stomach	stomach
16	chr5:16904600-16910400	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr5:16904600-16912400	Weak transcription	HSMM	muscle
18	chr5:16904800-16913600	Weak transcription	Fetal Muscle Trunk	muscle
19	chr5:16905200-16910400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr5:16905800-16911600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr5:16906200-16912400	Weak transcription	Stomach Smooth Muscle	stomach
22	chr5:16906400-16907800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr5:16906400-16909800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr5:16906400-16912400	Weak transcription	Fetal Intestine Small	intestine
25	chr5:16906400-16912800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr5:16906400-16912800	Weak transcription	Gastric	stomach
27	chr5:16906400-16913600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr5:16906600-16907800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr5:16906600-16908200	Enhancers	A549	lung
30	chr5:16906600-16909600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr5:16906600-16909600	Weak transcription	Fetal Muscle Leg	muscle
32	chr5:16906800-16909400	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr5:16906800-16909600	Weak transcription	Fetal Lung	lung
34	chr5:16906800-16909800	Weak transcription	Stomach Mucosa	stomach
35	chr5:16906800-16913600	Weak transcription	Psoas Muscle	Psoas
36	chr5:16907000-16908000	Weak transcription	Placenta	Placenta
37	chr5:16907000-16908600	Weak transcription	Duodenum Mucosa	Duodenum
38	chr5:16907000-16908800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr5:16907000-16909200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr5:16907000-16909400	Weak transcription	Pancreas	Pancrea
41	chr5:16907000-16910200	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr5:16907000-16911600	Weak transcription	Lung	lung
43	chr5:16907000-16912400	Weak transcription	Hela-S3	cervix
44	chr5:16907000-16913600	Weak transcription	Spleen	Spleen
45	chr5:16907400-16907600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr5:16907400-16907600	Enhancers	Ovary	ovary
47	chr5:16907400-16907600	Enhancers	Small Intestine	intestine
48	chr5:16907400-16907600	Enhancers	NHEK	skin
49	chr5:16907400-16908000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr5:16907400-16908000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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