Variant report

Variant	rs17055461
Chromosome Location	chr6:128545146-128545147
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10046162	0.82[EUR][1000 genomes]
rs10485161	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10485162	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10499136	0.82[EUR][1000 genomes]
rs10499138	1.00[EUR][1000 genomes]
rs11961948	1.00[AMR][1000 genomes]
rs11962332	1.00[AMR][1000 genomes]
rs11962916	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11968433	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11970637	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17053270	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17055290	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17055300	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17055360	1.00[EUR][1000 genomes]
rs17055365	1.00[EUR][1000 genomes]
rs17055403	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17055412	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17055415	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17055421	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17055443	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17055445	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17055488	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17055499	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17055501	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17055507	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1738273	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1768358	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1856497	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28874136	0.82[EUR][1000 genomes]
rs4131020	1.00[EUR][1000 genomes]
rs4496822	0.82[EUR][1000 genomes]
rs4895832	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4897244	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4897245	1.00[EUR][1000 genomes]
rs4897246	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4897247	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4897248	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4897249	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4897250	1.00[EUR][1000 genomes]
rs55828045	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56042959	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56932458	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57797601	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58652879	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58706847	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59341107	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60264538	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60436012	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61111040	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61757810	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6900798	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6904846	1.00[AMR][1000 genomes]
rs6905735	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6909380	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6910587	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6913738	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6918772	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6929394	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6929623	1.00[EUR][1000 genomes]
rs6931593	1.00[AMR][1000 genomes]
rs6933133	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6938199	1.00[EUR][1000 genomes]
rs73588698	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73590666	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73592613	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73592686	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73773990	0.82[EUR][1000 genomes]
rs7746423	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7751187	1.00[EUR][1000 genomes]
rs7752113	0.82[EUR][1000 genomes]
rs7754637	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7768121	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7772200	1.00[EUR][1000 genomes]
rs9491909	0.82[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	nsv1033443	chr6:128306654-128899203	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv538440	chr6:128306654-128899203	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv886649	chr6:128399657-128808054	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv604647	chr6:128421762-128547177	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv886651	chr6:128450019-128565778	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv886653	chr6:128455539-128555805	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv886654	chr6:128471938-128555805	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:128488200-128565200	Weak transcription	Fetal Stomach	stomach
2	chr6:128492600-128567800	Weak transcription	Ovary	ovary
3	chr6:128505800-128552200	Weak transcription	Duodenum Mucosa	Duodenum
4	chr6:128506000-128561000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr6:128520400-128573800	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr6:128522000-128560800	Weak transcription	Primary T cells from cord blood	blood
7	chr6:128527600-128561000	Weak transcription	Esophagus	oesophagus
8	chr6:128528200-128558400	Weak transcription	Brain Cingulate Gyrus	brain
9	chr6:128528400-128561000	Weak transcription	Fetal Brain Male	brain
10	chr6:128529400-128552600	Weak transcription	Small Intestine	intestine
11	chr6:128529800-128561000	Weak transcription	Stomach Smooth Muscle	stomach
12	chr6:128531000-128550600	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr6:128531000-128562400	Weak transcription	Aorta	Aorta
14	chr6:128531200-128554600	Weak transcription	Right Ventricle	heart
15	chr6:128531200-128562400	Weak transcription	HSMMtube	muscle
16	chr6:128531200-128567800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:128531200-128573800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr6:128531400-128553600	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr6:128532000-128545600	Weak transcription	NHEK	skin
20	chr6:128532000-128554400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr6:128532000-128561000	Weak transcription	Osteobl	bone
22	chr6:128532200-128553200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr6:128536000-128554800	Weak transcription	Brain Substantia Nigra	brain
24	chr6:128536800-128560600	Weak transcription	Fetal Lung	lung
25	chr6:128537200-128561000	Weak transcription	Fetal Muscle Leg	muscle
26	chr6:128537600-128573800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr6:128539800-128552400	Weak transcription	Liver	Liver
28	chr6:128539800-128558200	Weak transcription	NH-A	brain
29	chr6:128540000-128547200	Weak transcription	HMEC	breast
30	chr6:128540200-128552800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr6:128540200-128556600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr6:128540200-128559600	Weak transcription	Primary B cells from peripheral blood	blood
33	chr6:128540200-128561000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr6:128540200-128564800	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr6:128540400-128545600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr6:128540400-128551200	Weak transcription	HSMM	muscle
37	chr6:128540400-128554400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr6:128540400-128560400	Weak transcription	Fetal Thymus	thymus
39	chr6:128540400-128560400	Weak transcription	HUVEC	blood vessel
40	chr6:128540400-128569400	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr6:128540600-128550200	Weak transcription	Fetal Intestine Large	intestine
42	chr6:128540600-128561000	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr6:128540800-128562400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr6:128541000-128545400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr6:128541000-128551200	Weak transcription	Primary B cells from cord blood	blood
46	chr6:128541200-128547000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr6:128542400-128551000	Weak transcription	HepG2	liver
48	chr6:128543800-128545600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr6:128543800-128550200	Weak transcription	Stomach Mucosa	stomach
50	chr6:128544000-128556600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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