Variant report

Variant	rs7385009
Chromosome Location	chr7:48136339-48136340
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	chr7:48134492..48136444-chr7:48138845..48140444,2	MCF-7	breast:

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11768083	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs13228276	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3752889	0.81[AMR][1000 genomes]
rs3752890	0.81[AMR][1000 genomes]
rs3763505	0.80[AMR][1000 genomes]
rs6463462	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7341420	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7459020	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7804178	0.81[AFR][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	nsv1026223	chr7:47560728-48243287	Genic enhancers Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv869585	chr7:47765428-48151324	Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv532120	chr7:47882757-48195869	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv470221	chr7:47917495-48354363	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv464442	chr7:47917495-48354820	Genic enhancers Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv606893	chr7:47917495-48354820	Flanking Active TSS Strong transcription Genic enhancers Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv1027414	chr7:48117684-48438543	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	esv997355	chr7:48128431-48138826	Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Weak transcription Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7385009	UPP1	cis	Muscle Skeletal	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:48129000-48137000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr7:48129600-48141000	Weak transcription	Gastric	stomach
3	chr7:48129600-48141200	Weak transcription	Ovary	ovary
4	chr7:48130200-48138200	Weak transcription	Pancreas	Pancrea
5	chr7:48130200-48141400	Weak transcription	Brain Substantia Nigra	brain
6	chr7:48130200-48146800	Weak transcription	Colon Smooth Muscle	Colon
7	chr7:48130200-48148200	Weak transcription	Right Atrium	heart
8	chr7:48130400-48137000	Weak transcription	Primary B cells from peripheral blood	blood
9	chr7:48130400-48141400	Weak transcription	HepG2	liver
10	chr7:48130400-48149800	Weak transcription	Fetal Kidney	kidney
11	chr7:48130400-48150000	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr7:48130600-48139200	Genic enhancers	Placenta	Placenta
13	chr7:48130600-48143600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr7:48130800-48149200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr7:48131000-48137800	Strong transcription	Fetal Intestine Small	intestine
16	chr7:48131000-48145200	Strong transcription	Rectal Mucosa Donor 31	rectum
17	chr7:48131000-48149200	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr7:48131200-48138800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr7:48131200-48145000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr7:48131200-48148800	Strong transcription	H1 Cell Line	embryonic stem cell
21	chr7:48131200-48149200	Strong transcription	Duodenum Mucosa	Duodenum
22	chr7:48131400-48136400	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr7:48131400-48136600	Strong transcription	H9 Cell Line	embryonic stem cell
24	chr7:48131400-48139800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr7:48131400-48149000	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr7:48131400-48149400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr7:48131600-48138400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr7:48131600-48139200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr7:48131600-48142200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr7:48131600-48148800	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr7:48131600-48149000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr7:48131600-48149600	Weak transcription	Thymus	Thymus
33	chr7:48132000-48137600	Weak transcription	Psoas Muscle	Psoas
34	chr7:48132000-48138200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
35	chr7:48132000-48139600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr7:48132200-48137000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr7:48132200-48137600	Genic enhancers	HMEC	breast
38	chr7:48132200-48146400	Weak transcription	Small Intestine	intestine
39	chr7:48132200-48149200	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr7:48133200-48137000	Enhancers	Primary T killer memory cells from peripheral blood	blood
41	chr7:48133200-48141200	Weak transcription	Fetal Intestine Large	intestine
42	chr7:48133400-48141200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr7:48133400-48141200	Weak transcription	Brain Anterior Caudate	brain
44	chr7:48133400-48141400	Weak transcription	Rectal Smooth Muscle	rectum
45	chr7:48133600-48137200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr7:48133800-48136400	Genic enhancers	Spleen	Spleen
47	chr7:48133800-48136400	Genic enhancers	NHDF-Ad	bronchial
48	chr7:48133800-48138600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr7:48134000-48137000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
50	chr7:48134000-48137400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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