Variant report

Variant	rs72808943
Chromosome Location	chr5:115641857-115641858
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	CTCF	chr5:115641760-115641910	HCPEpiC	choroid plexus:	n/a	chr5:115641778-115641786

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LVRN.1-4	chr5:115641553-115642622	NONHSAT103359

Variant related genes	Relation type
ENSG00000250015	TF binding region

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10519452	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17139251	0.87[EUR][1000 genomes]
rs17139353	0.87[ASN][1000 genomes]
rs17139524	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17139532	0.80[EUR][1000 genomes]
rs2900096	0.80[ASN][1000 genomes]
rs4308513	0.82[ASN][1000 genomes]
rs55742067	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55857351	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs57659470	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs58424191	0.93[ASN][1000 genomes]
rs66783056	0.87[EUR][1000 genomes]
rs67139169	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs67339497	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67412230	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72804862	0.85[EUR][1000 genomes]
rs72804864	0.85[EUR][1000 genomes]
rs72804867	0.85[EUR][1000 genomes]
rs72804869	0.85[EUR][1000 genomes]
rs72804873	0.85[EUR][1000 genomes]
rs72804875	0.85[EUR][1000 genomes]
rs72804882	0.85[EUR][1000 genomes]
rs72804884	0.85[EUR][1000 genomes]
rs72804885	0.85[EUR][1000 genomes]
rs72804889	0.87[EUR][1000 genomes]
rs72804891	0.85[EUR][1000 genomes]
rs72804893	0.85[EUR][1000 genomes]
rs72804896	0.87[EUR][1000 genomes]
rs72804899	0.87[EUR][1000 genomes]
rs72804900	0.85[EUR][1000 genomes]
rs72806907	0.82[EUR][1000 genomes]
rs72806908	0.87[EUR][1000 genomes]
rs72806910	0.85[EUR][1000 genomes]
rs72806917	0.87[EUR][1000 genomes]
rs72806919	0.87[EUR][1000 genomes]
rs72806920	0.87[EUR][1000 genomes]
rs72806923	0.87[EUR][1000 genomes]
rs72806926	0.87[EUR][1000 genomes]
rs72806927	0.87[EUR][1000 genomes]
rs72806930	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72806931	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72806933	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72806937	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72806941	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72806944	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72808904	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72808909	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72808912	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72808916	0.87[ASN][1000 genomes]
rs72808917	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72808922	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72808927	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72808928	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72808929	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72808930	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72808931	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72808932	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72808934	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72808945	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72808949	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72808952	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72808958	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72808959	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72808960	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72808961	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72808964	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72808969	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72808973	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7715621	0.82[ASN][1000 genomes]
rs7729344	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34146	chr5:115315944-115729919	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	esv2755349	chr5:115384101-115733101	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv882746	chr5:115566026-115704566	Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv882747	chr5:115566636-115662510	Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1017983	chr5:115578765-115713688	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv882748	chr5:115584159-115669950	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv869754	chr5:115634234-115696094	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv4968	chr5:115635771-115714856	Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent/Poised TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv1018001	chr5:115640603-115660285	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:115625600-115643000	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr5:115626800-115642200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr5:115628000-115643800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr5:115628600-115643400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr5:115629000-115643800	Weak transcription	HUVEC	blood vessel
6	chr5:115632000-115643000	Weak transcription	NH-A	brain
7	chr5:115632600-115643400	Weak transcription	Stomach Mucosa	stomach
8	chr5:115632800-115642600	Weak transcription	NHDF-Ad	bronchial
9	chr5:115634200-115642200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr5:115634200-115643600	Weak transcription	HepG2	liver
11	chr5:115634200-115664400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr5:115634400-115645600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr5:115635400-115642400	Strong transcription	Rectal Mucosa Donor 31	rectum
14	chr5:115635400-115642600	Strong transcription	Left Ventricle	heart
15	chr5:115635400-115643600	Strong transcription	Fetal Intestine Large	intestine
16	chr5:115636200-115643600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr5:115637600-115643400	Strong transcription	Primary T helper cells PMA-I stimulated	--
18	chr5:115637600-115643800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr5:115637800-115642400	Enhancers	Liver	Liver
20	chr5:115637800-115642800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr5:115638200-115642600	Strong transcription	Skeletal Muscle Female	skeletal muscle
22	chr5:115638200-115642800	Strong transcription	Pancreas	Pancrea
23	chr5:115638400-115643000	Strong transcription	Right Ventricle	heart
24	chr5:115638400-115643400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr5:115638400-115644000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr5:115638800-115643400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr5:115639000-115644400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr5:115639200-115642000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr5:115639200-115642000	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr5:115639200-115643200	Strong transcription	Placenta	Placenta
31	chr5:115639400-115642800	Strong transcription	A549	lung
32	chr5:115639400-115643000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr5:115639400-115645200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
34	chr5:115639600-115642200	Strong transcription	Skeletal Muscle Male	skeletal muscle
35	chr5:115639600-115642800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr5:115639600-115643000	Strong transcription	Primary neutrophils fromperipheralblood	blood
37	chr5:115639600-115643600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr5:115639600-115647400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr5:115639800-115642600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
40	chr5:115639800-115643000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr5:115639800-115643400	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr5:115640000-115644200	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr5:115640200-115642600	Strong transcription	HSMMtube	muscle
44	chr5:115640200-115643600	Strong transcription	Stomach Smooth Muscle	stomach
45	chr5:115640200-115645600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
46	chr5:115640200-115647200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
47	chr5:115640400-115642000	Strong transcription	Brain Hippocampus Middle	brain
48	chr5:115640400-115643000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr5:115640400-115643000	ZNF genes & repeats	Fetal Intestine Small	intestine
50	chr5:115640400-115643200	ZNF genes & repeats	Aorta	Aorta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links