Variant report

Variant	rs71587641
Chromosome Location	chr5:16903140-16903141
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	MYC	chr5:16902927-16903400	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr5:16903062-16903259	MCF10A-Er-Src	breast:	n/a	n/a
3	STAT3	chr5:16903098-16903366	MCF10A-Er-Src	breast:	n/a	n/a
4	MYC	chr5:16902920-16903394	MCF10A-Er-Src	breast:	n/a	n/a
5	STAT3	chr5:16902996-16903392	MCF10A-Er-Src	breast:	n/a	n/a
6	STAT3	chr5:16902997-16903319	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr5:16902277-16903286	SK-N-MC	brain:	n/a	n/a
8	FOS	chr5:16902907-16903423	MCF10A-Er-Src	breast:	n/a	n/a
9	FOS	chr5:16902927-16903383	MCF10A-Er-Src	breast:	n/a	n/a
10	FOS	chr5:16902992-16903328	MCF10A-Er-Src	breast:	n/a	n/a
11	FOS	chr5:16902918-16903407	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
ENSG00000243538	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10045785	0.81[ASN][1000 genomes]
rs10059594	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10520847	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13176126	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16869222	0.81[ASN][1000 genomes]
rs173789	0.81[ASN][1000 genomes]
rs17651643	0.81[ASN][1000 genomes]
rs4438877	0.91[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs55900559	0.81[ASN][1000 genomes]
rs58057438	0.81[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:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:16896000-16912400	Weak transcription	Esophagus	oesophagus
2	chr5:16898200-16903400	Weak transcription	Placenta	Placenta
3	chr5:16898200-16903800	Weak transcription	Osteobl	bone
4	chr5:16898200-16904000	Weak transcription	NHLF	lung
5	chr5:16898200-16906200	Weak transcription	Psoas Muscle	Psoas
6	chr5:16898200-16912600	Weak transcription	NH-A	brain
7	chr5:16898400-16903800	Weak transcription	Small Intestine	intestine
8	chr5:16898400-16904600	Weak transcription	Fetal Intestine Small	intestine
9	chr5:16899400-16907000	Enhancers	Pancreas	Pancrea
10	chr5:16899800-16905600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr5:16899800-16910000	Weak transcription	HUVEC	blood vessel
12	chr5:16899800-16910800	Weak transcription	HMEC	breast
13	chr5:16900400-16905400	Enhancers	Fetal Muscle Leg	muscle
14	chr5:16900600-16903800	Weak transcription	NHDF-Ad	bronchial
15	chr5:16900600-16903800	Weak transcription	NHEK	skin
16	chr5:16900800-16903200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr5:16900800-16903200	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr5:16901200-16904400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr5:16901200-16904800	Enhancers	Fetal Muscle Trunk	muscle
20	chr5:16901200-16906400	Enhancers	Gastric	stomach
21	chr5:16901200-16907000	Enhancers	Lung	lung
22	chr5:16901400-16903800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr5:16901400-16906400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr5:16901400-16907600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr5:16901600-16905200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr5:16901600-16906000	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr5:16901600-16907600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr5:16901600-16909400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr5:16902000-16903200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr5:16902000-16903600	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr5:16902000-16903600	Weak transcription	Duodenum Mucosa	Duodenum
32	chr5:16902000-16903800	Enhancers	A549	lung
33	chr5:16902000-16903800	Weak transcription	Hela-S3	cervix
34	chr5:16902000-16904000	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr5:16902000-16905200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr5:16902000-16905400	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr5:16902000-16905400	Weak transcription	Spleen	Spleen
38	chr5:16902000-16906200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr5:16902000-16906200	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr5:16902000-16912800	Weak transcription	Fetal Intestine Large	intestine
41	chr5:16902200-16904200	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr5:16902200-16906600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr5:16902200-16913800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr5:16902200-16919000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr5:16902200-16930000	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr5:16902400-16904600	Enhancers	HSMMtube	muscle
47	chr5:16902400-16907000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr5:16902600-16903800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr5:16902600-16904600	Enhancers	Muscle Satellite Cultured Cells	--
50	chr5:16902800-16904400	Enhancers	Stomach Mucosa	stomach

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