Variant report

Variant	rs835729
Chromosome Location	chr5:79723402-79723403
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:79686081..79688375-chr5:79722309..79724181,2	K562	blood:
2	chr5:79701298..79704243-chr5:79720985..79723593,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000039319	Chromatin interaction

Extended variants
information (count: 121 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs10433	0.87[ASN][1000 genomes]
rs10474621	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10942926	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1097307	0.97[ASN][1000 genomes]
rs1097308	0.97[ASN][1000 genomes]
rs1097309	0.97[ASN][1000 genomes]
rs1102116	0.87[ASN][1000 genomes]
rs1103116	0.95[ASN][1000 genomes]
rs1104243	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13354660	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13359253	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1363775	0.92[ASN][1000 genomes]
rs1423113	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16877755	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16877757	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs168938	0.97[ASN][1000 genomes]
rs168939	0.92[ASN][1000 genomes]
rs168940	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs171595	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs171596	0.89[AFR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs171821	0.92[ASN][1000 genomes]
rs173597	0.87[ASN][1000 genomes]
rs173598	0.84[AFR][1000 genomes]
rs173599	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs174075	0.92[ASN][1000 genomes]
rs174076	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1820119	0.92[ASN][1000 genomes]
rs185100	0.89[ASN][1000 genomes]
rs187478	0.87[ASN][1000 genomes]
rs187479	0.87[ASN][1000 genomes]
rs192313	1.00[ASN][1000 genomes]
rs194540	0.81[ASN][1000 genomes]
rs194541	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2251759	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs248999	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs249001	0.87[ASN][1000 genomes]
rs249003	0.87[ASN][1000 genomes]
rs249004	0.89[AFR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs249005	0.87[ASN][1000 genomes]
rs249006	0.83[AFR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs249016	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs249020	0.80[ASN][1000 genomes]
rs249021	0.89[ASN][1000 genomes]
rs249023	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs249024	0.92[ASN][1000 genomes]
rs249025	0.92[ASN][1000 genomes]
rs249026	0.92[ASN][1000 genomes]
rs249027	0.92[ASN][1000 genomes]
rs249028	0.92[ASN][1000 genomes]
rs249029	0.87[ASN][1000 genomes]
rs249030	0.91[AFR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs249031	0.87[ASN][1000 genomes]
rs249032	0.89[AFR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs249037	0.87[ASN][1000 genomes]
rs249038	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs249039	0.92[ASN][1000 genomes]
rs2544591	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2544592	0.97[ASN][1000 genomes]
rs2544593	0.97[ASN][1000 genomes]
rs2544598	0.92[ASN][1000 genomes]
rs2544599	0.92[ASN][1000 genomes]
rs2544600	0.92[ASN][1000 genomes]
rs2544603	0.92[ASN][1000 genomes]
rs2544604	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2547487	0.97[ASN][1000 genomes]
rs259023	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs259024	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs259025	0.97[ASN][1000 genomes]
rs259026	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs259027	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs259028	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs259029	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs259030	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs259031	0.92[ASN][1000 genomes]
rs259032	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs259033	0.92[ASN][1000 genomes]
rs259034	0.92[ASN][1000 genomes]
rs259036	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs259037	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs259038	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs259039	0.92[ASN][1000 genomes]
rs259040	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs259041	0.92[ASN][1000 genomes]
rs259042	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs259043	0.92[ASN][1000 genomes]
rs259044	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs259045	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs259046	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs259047	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs259048	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs259051	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs259052	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs259053	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs259054	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs259055	0.97[ASN][1000 genomes]
rs2599508	0.87[ASN][1000 genomes]
rs28496723	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28555465	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3095851	0.92[ASN][1000 genomes]
rs3096109	0.88[AFR][1000 genomes]
rs3096111	0.92[ASN][1000 genomes]
rs394076	0.87[ASN][1000 genomes]
rs394170	0.87[ASN][1000 genomes]
rs399261	0.87[ASN][1000 genomes]
rs401612	0.92[ASN][1000 genomes]
rs408899	0.87[ASN][1000 genomes]
rs4704674	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs557346	0.86[AFR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6869519	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6885891	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6887302	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs701380	0.87[ASN][1000 genomes]
rs835726	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs835728	0.86[ASN][1000 genomes]
rs856765	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs856772	0.88[AFR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs863163	0.87[ASN][1000 genomes]
rs969567	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948807	chr5:79549207-79805765	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv518480	chr5:79586085-79748382	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv1028027	chr5:79694699-79841752	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79704600-79723600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:79704600-79730200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr5:79704600-79730200	Weak transcription	Lung	lung
4	chr5:79704600-79758000	Weak transcription	Spleen	Spleen
5	chr5:79704600-79758600	Weak transcription	Gastric	stomach
6	chr5:79704800-79731600	Weak transcription	Fetal Thymus	thymus
7	chr5:79705600-79731200	Weak transcription	Aorta	Aorta
8	chr5:79705600-79757400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr5:79705800-79730200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr5:79705800-79731400	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr5:79705800-79731800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr5:79706000-79731400	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr5:79706000-79731800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr5:79706000-79732000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr5:79706000-79732000	Weak transcription	NHLF	lung
16	chr5:79706200-79731600	Weak transcription	NHDF-Ad	bronchial
17	chr5:79707800-79731600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr5:79707800-79731800	Weak transcription	Brain Angular Gyrus	brain
19	chr5:79707800-79735400	Weak transcription	Hela-S3	cervix
20	chr5:79708000-79730200	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr5:79708000-79730200	Weak transcription	Liver	Liver
22	chr5:79708000-79730200	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr5:79708000-79731400	Weak transcription	Adipose Nuclei	Adipose
24	chr5:79708000-79731400	Weak transcription	Left Ventricle	heart
25	chr5:79708000-79731400	Weak transcription	Ovary	ovary
26	chr5:79708000-79731800	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr5:79708000-79738200	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr5:79708000-79739200	Weak transcription	Right Ventricle	heart
29	chr5:79710400-79731800	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr5:79710400-79732000	Weak transcription	A549	lung
31	chr5:79710600-79731400	Weak transcription	Primary B cells from cord blood	blood
32	chr5:79713400-79731400	Weak transcription	Brain Substantia Nigra	brain
33	chr5:79715600-79730000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr5:79718200-79731800	Weak transcription	NH-A	brain
35	chr5:79718600-79730200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr5:79719800-79730200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr5:79720400-79730000	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr5:79720400-79730400	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr5:79720400-79731000	Weak transcription	Fetal Intestine Large	intestine
40	chr5:79720400-79743200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr5:79720800-79731200	Weak transcription	Primary B cells from peripheral blood	blood
42	chr5:79721000-79724000	Weak transcription	Fetal Lung	lung
43	chr5:79721000-79731400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr5:79721000-79731400	Weak transcription	HepG2	liver
45	chr5:79721200-79730200	Weak transcription	Fetal Muscle Trunk	muscle
46	chr5:79721800-79731600	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr5:79722000-79730200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr5:79722200-79724400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr5:79722400-79724000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr5:79722400-79733400	Weak transcription	H1 Cell Line	embryonic stem cell

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