Variant report

Variant	rs10059594
Chromosome Location	chr5:16904905-16904906
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	POLR2A	chr5:16903776-16907066	SK-N-MC	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:16899974..16902321-chr5:16904564..16907062,3	MCF-7	breast:
2	chr5:16894491..16896403-chr5:16903844..16905936,2	MCF-7	breast:
3	chr5:16903174..16906084-chr5:16912041..16914007,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000243538	TF binding region

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs10520847	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13176126	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71587641	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
7	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:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:16896000-16912400	Weak transcription	Esophagus	oesophagus
2	chr5:16898200-16906200	Weak transcription	Psoas Muscle	Psoas
3	chr5:16898200-16912600	Weak transcription	NH-A	brain
4	chr5:16899400-16907000	Enhancers	Pancreas	Pancrea
5	chr5:16899800-16905600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr5:16899800-16910000	Weak transcription	HUVEC	blood vessel
7	chr5:16899800-16910800	Weak transcription	HMEC	breast
8	chr5:16900400-16905400	Enhancers	Fetal Muscle Leg	muscle
9	chr5:16901200-16906400	Enhancers	Gastric	stomach
10	chr5:16901200-16907000	Enhancers	Lung	lung
11	chr5:16901400-16906400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr5:16901400-16907600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr5:16901600-16905200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr5:16901600-16906000	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr5:16901600-16907600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr5:16901600-16909400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr5:16902000-16905200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr5:16902000-16905400	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr5:16902000-16905400	Weak transcription	Spleen	Spleen
20	chr5:16902000-16906200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr5:16902000-16906200	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr5:16902000-16912800	Weak transcription	Fetal Intestine Large	intestine
23	chr5:16902200-16906600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr5:16902200-16913800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr5:16902200-16919000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr5:16902200-16930000	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr5:16902400-16907000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr5:16902800-16906600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr5:16903000-16905200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr5:16903000-16907000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr5:16903200-16905200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr5:16903400-16907000	Enhancers	Placenta	Placenta
33	chr5:16903800-16905800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr5:16904200-16905200	Weak transcription	Ovary	ovary
35	chr5:16904200-16906000	Weak transcription	Stomach Smooth Muscle	stomach
36	chr5:16904200-16906000	Weak transcription	Hela-S3	cervix
37	chr5:16904400-16905200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr5:16904400-16905200	Weak transcription	Stomach Mucosa	stomach
39	chr5:16904400-16905400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr5:16904400-16905800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr5:16904400-16906000	Strong transcription	NHEK	skin
42	chr5:16904400-16906400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr5:16904400-16906600	Weak transcription	Duodenum Mucosa	Duodenum
44	chr5:16904400-16907400	Weak transcription	Small Intestine	intestine
45	chr5:16904400-16912400	Weak transcription	NHDF-Ad	bronchial
46	chr5:16904400-16912400	Weak transcription	NHLF	lung
47	chr5:16904400-16912400	Weak transcription	Osteobl	bone
48	chr5:16904400-16933200	Weak transcription	Fetal Stomach	stomach
49	chr5:16904600-16905800	Strong transcription	Fetal Intestine Small	intestine
50	chr5:16904600-16905800	Enhancers	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links