Variant report

Variant	rs4720625
Chromosome Location	chr7:47996557-47996558
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PKD1L1-1	chr7:47994962-47996911	NONHSAT120522
2	lnc-C7orf57-1	chr7:47996390-47996915	NONHSAT120523

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10261436	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10499669	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12667562	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12669119	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17131948	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2307252	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2348665	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3176491	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3176568	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3176581	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3176595	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36213466	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56075223	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59023024	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59920101	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62447088	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62447089	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62447093	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73695940	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs885338	1.00[AMR][1000 genomes];0.98[EUR][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	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	nsv830991	chr7:47854530-48025996	Weak transcription Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:47934000-48001800	Weak transcription	Psoas Muscle	Psoas
2	chr7:47977400-48000600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr7:47982000-47999400	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr7:47983600-48001000	Weak transcription	NHLF	lung
5	chr7:47985000-48001400	Weak transcription	Hela-S3	cervix
6	chr7:47985600-48000600	Weak transcription	Ovary	ovary
7	chr7:47986400-48003800	Weak transcription	Fetal Brain Male	brain
8	chr7:47986800-48001800	Weak transcription	NHEK	skin
9	chr7:47990000-48000600	Weak transcription	Brain Angular Gyrus	brain
10	chr7:47990600-48000600	Weak transcription	Brain Cingulate Gyrus	brain
11	chr7:47991000-48001400	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr7:47991400-48001000	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr7:47991400-48003600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr7:47991400-48004800	Weak transcription	Fetal Kidney	kidney
15	chr7:47991600-48000600	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr7:47991600-48000600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr7:47992000-48000400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr7:47992000-48000600	Weak transcription	Brain Germinal Matrix	brain
19	chr7:47992000-48001600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr7:47992000-48001600	Weak transcription	Pancreas	Pancrea
21	chr7:47992000-48002400	Weak transcription	HepG2	liver
22	chr7:47992000-48004400	Weak transcription	Stomach Mucosa	stomach
23	chr7:47992200-48005200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr7:47992400-48000200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr7:47992400-48000400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr7:47992400-48000600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr7:47992600-47996800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr7:47992600-47996800	Strong transcription	Primary B cells from cord blood	blood
29	chr7:47992600-48000400	Weak transcription	Fetal Brain Female	brain
30	chr7:47992800-48000600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr7:47993000-47997000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr7:47993200-47997200	Strong transcription	Liver	Liver
33	chr7:47993200-47997400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr7:47993200-47998000	Strong transcription	Fetal Muscle Trunk	muscle
35	chr7:47993200-47998400	Strong transcription	Primary T cells from cord blood	blood
36	chr7:47993200-48000600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr7:47993400-47997000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr7:47993600-47997000	Strong transcription	Brain Inferior Temporal Lobe	brain
39	chr7:47993600-47997400	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr7:47993600-47998200	Strong transcription	Adipose Nuclei	Adipose
41	chr7:47993800-47996800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr7:47993800-47997000	Strong transcription	Duodenum Smooth Muscle	Duodenum
43	chr7:47993800-47997000	Strong transcription	Placenta	Placenta
44	chr7:47993800-47997400	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr7:47993800-47997400	Strong transcription	Fetal Lung	lung
46	chr7:47993800-47998000	Strong transcription	HUES6 Cell Line	embryonic stem cell
47	chr7:47993800-47998000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
48	chr7:47993800-47998200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr7:47994000-47996800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr7:47994000-47996800	Strong transcription	Rectal Mucosa Donor 31	rectum

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