Variant report

Variant	rs3096111
Chromosome Location	chr5:79717928-79717929
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 119 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:116)

rs_ID	r²[population]
rs10052497	0.80[EUR][1000 genomes]
rs10433	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10474621	0.82[ASN][1000 genomes]
rs10942926	0.85[ASN][1000 genomes]
rs1097307	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1097308	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1097309	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1102116	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1103116	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1363775	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1423113	0.87[ASN][1000 genomes]
rs16877755	0.82[ASN][1000 genomes]
rs16877757	0.82[ASN][1000 genomes]
rs168938	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs168939	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs168940	0.90[ASN][1000 genomes]
rs171595	0.80[ASN][1000 genomes]
rs171596	0.80[ASN][1000 genomes]
rs171821	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs173597	0.80[ASN][1000 genomes]
rs173599	0.85[ASN][1000 genomes]
rs174075	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs174076	0.87[ASN][1000 genomes]
rs1820119	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs185100	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs187478	0.80[ASN][1000 genomes]
rs187479	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs192313	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs194541	0.87[ASN][1000 genomes]
rs2112152	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2251759	0.85[ASN][1000 genomes]
rs248999	0.80[ASN][1000 genomes]
rs249001	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs249003	0.80[ASN][1000 genomes]
rs249004	0.80[ASN][1000 genomes]
rs249005	0.80[ASN][1000 genomes]
rs249006	0.80[ASN][1000 genomes]
rs249016	0.82[ASN][1000 genomes]
rs249020	0.83[EUR][1000 genomes]
rs249021	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs249023	0.85[ASN][1000 genomes]
rs249024	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs249025	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs249026	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs249027	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs249028	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs249029	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs249030	0.80[ASN][1000 genomes]
rs249031	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs249032	0.80[ASN][1000 genomes]
rs249037	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs249038	0.85[ASN][1000 genomes]
rs249039	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2544591	0.90[ASN][1000 genomes]
rs2544592	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2544593	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2544598	0.85[AFR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2544599	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2544600	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2544603	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2544604	0.85[ASN][1000 genomes]
rs2547487	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2547497	0.82[EUR][1000 genomes]
rs259023	0.95[ASN][1000 genomes]
rs259024	0.95[ASN][1000 genomes]
rs259025	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs259026	0.95[ASN][1000 genomes]
rs259027	0.95[ASN][1000 genomes]
rs259028	0.85[ASN][1000 genomes]
rs259029	0.85[ASN][1000 genomes]
rs259030	0.85[ASN][1000 genomes]
rs259031	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs259032	0.85[ASN][1000 genomes]
rs259033	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs259034	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs259035	0.82[EUR][1000 genomes]
rs259036	0.87[ASN][1000 genomes]
rs259037	0.87[ASN][1000 genomes]
rs259038	0.87[ASN][1000 genomes]
rs259039	0.90[ASN][1000 genomes]
rs259040	0.90[ASN][1000 genomes]
rs259041	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs259042	0.90[ASN][1000 genomes]
rs259043	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs259044	0.90[ASN][1000 genomes]
rs259045	0.90[ASN][1000 genomes]
rs259046	0.90[ASN][1000 genomes]
rs259047	0.90[ASN][1000 genomes]
rs259048	0.90[ASN][1000 genomes]
rs259051	0.90[ASN][1000 genomes]
rs259052	0.87[ASN][1000 genomes]
rs259053	0.90[ASN][1000 genomes]
rs259054	0.90[ASN][1000 genomes]
rs259055	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2599508	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28496723	0.85[ASN][1000 genomes]
rs28555465	0.85[ASN][1000 genomes]
rs3095851	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3096112	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs394076	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs394170	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs399261	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs401612	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs408899	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4704674	0.85[ASN][1000 genomes]
rs557346	0.80[ASN][1000 genomes]
rs6869519	0.82[ASN][1000 genomes]
rs6885891	0.87[ASN][1000 genomes]
rs701380	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs835726	0.92[ASN][1000 genomes]
rs835729	0.92[ASN][1000 genomes]
rs835731	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs856765	0.85[ASN][1000 genomes]
rs856772	0.80[ASN][1000 genomes]
rs863163	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs969567	0.91[EUR][1000 genomes];0.85[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:50 , 50 per page) page: 1

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	chr5:79705800-79723400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr5:79705800-79730200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr5:79705800-79731400	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr5:79705800-79731800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr5:79706000-79718000	Weak transcription	Duodenum Mucosa	Duodenum
14	chr5:79706000-79731400	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr5:79706000-79731800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr5:79706000-79732000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr5:79706000-79732000	Weak transcription	NHLF	lung
18	chr5:79706200-79722000	Weak transcription	Brain Germinal Matrix	brain
19	chr5:79706200-79722200	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr5:79706200-79731600	Weak transcription	NHDF-Ad	bronchial
21	chr5:79706400-79720000	Weak transcription	Fetal Lung	lung
22	chr5:79707800-79731600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr5:79707800-79731800	Weak transcription	Brain Angular Gyrus	brain
24	chr5:79707800-79735400	Weak transcription	Hela-S3	cervix
25	chr5:79708000-79719600	Weak transcription	Brain Anterior Caudate	brain
26	chr5:79708000-79730200	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr5:79708000-79730200	Weak transcription	Liver	Liver
28	chr5:79708000-79730200	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr5:79708000-79731400	Weak transcription	Adipose Nuclei	Adipose
30	chr5:79708000-79731400	Weak transcription	Left Ventricle	heart
31	chr5:79708000-79731400	Weak transcription	Ovary	ovary
32	chr5:79708000-79731800	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr5:79708000-79738200	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr5:79708000-79739200	Weak transcription	Right Ventricle	heart
35	chr5:79709000-79718000	Weak transcription	Fetal Muscle Leg	muscle
36	chr5:79709000-79718200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr5:79709000-79723400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr5:79709200-79718200	Weak transcription	Fetal Stomach	stomach
39	chr5:79710400-79731800	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr5:79710400-79732000	Weak transcription	A549	lung
41	chr5:79710600-79731400	Weak transcription	Primary B cells from cord blood	blood
42	chr5:79711000-79720000	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr5:79713400-79731400	Weak transcription	Brain Substantia Nigra	brain
44	chr5:79715000-79718000	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr5:79715400-79718200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr5:79715400-79722800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr5:79715600-79730000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr5:79715800-79718200	Weak transcription	Fetal Intestine Small	intestine
49	chr5:79716200-79718000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr5:79717600-79718600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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