Variant report

Variant	rs73890767
Chromosome Location	chr3:195043177-195043178
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-XXYLT1-5	chr3:195042533-195043708	ucscGeneNc_uc003fto_1

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11917903	1.00[AMR][1000 genomes]
rs11918729	1.00[AMR][1000 genomes]
rs11926961	1.00[AMR][1000 genomes]
rs2095969	1.00[AMR][1000 genomes]
rs55716204	1.00[AMR][1000 genomes]
rs56309159	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56911559	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57367947	1.00[AMR][1000 genomes]
rs58212573	1.00[AMR][1000 genomes]
rs58381246	1.00[AMR][1000 genomes]
rs58471352	1.00[AMR][1000 genomes]
rs59751965	1.00[AFR][1000 genomes]
rs60222890	1.00[AMR][1000 genomes]
rs60284665	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60560609	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60584652	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6437461	1.00[AMR][1000 genomes]
rs6764918	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6779124	1.00[AMR][1000 genomes]
rs6779129	1.00[AMR][1000 genomes]
rs6779217	1.00[AMR][1000 genomes]
rs6790118	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6790784	1.00[AMR][1000 genomes]
rs6809102	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73067069	1.00[AMR][1000 genomes]
rs73067076	1.00[AMR][1000 genomes]
rs73067078	1.00[AMR][1000 genomes]
rs73067082	1.00[AMR][1000 genomes]
rs73067084	1.00[AMR][1000 genomes]
rs73890752	0.93[AFR][1000 genomes]
rs73890762	1.00[AFR][1000 genomes]
rs73890763	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73890764	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73890778	1.00[AMR][1000 genomes]
rs73890782	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73890784	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73890791	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73890793	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73890826	1.00[AMR][1000 genomes]
rs73890827	1.00[AMR][1000 genomes]
rs73893622	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73893623	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73893628	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7611086	0.93[AFR][1000 genomes]
rs7649610	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009796	chr3:194737333-195124248	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
2	nsv1014826	chr3:194834615-195631793	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
3	nsv536876	chr3:194834615-195631793	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
4	nsv533904	chr3:194868329-195438728	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	65 gene(s)	inside rSNPs	diseases
5	nsv1010168	chr3:194874494-195135790	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv536877	chr3:194874494-195135790	Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv997956	chr3:194879534-195087539	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	nsv536878	chr3:194879534-195087539	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers 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	20 gene(s)	inside rSNPs	diseases
9	esv1832781	chr3:194902818-195528226	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases
10	nsv432508	chr3:194916131-195478861	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	59 gene(s)	inside rSNPs	diseases
11	nsv432510	chr3:194935314-195478861	Weak transcription Enhancers Strong transcription Active TSS Flanking 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 miRNA	59 gene(s)	inside rSNPs	diseases
12	nsv1005519	chr3:194964301-195340515	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
13	nsv432511	chr3:194986167-195479748	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
14	nsv432512	chr3:195007260-195475989	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	54 gene(s)	inside rSNPs	diseases
15	nsv526569	chr3:195038287-195123495	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:194992600-195090000	Weak transcription	Aorta	Aorta
2	chr3:194993000-195050400	Weak transcription	Colon Smooth Muscle	Colon
3	chr3:194993000-195076000	Weak transcription	Fetal Heart	heart
4	chr3:195004000-195066600	Weak transcription	Small Intestine	intestine
5	chr3:195010000-195061000	Weak transcription	Fetal Kidney	kidney
6	chr3:195010000-195076400	Weak transcription	Brain Angular Gyrus	brain
7	chr3:195022600-195073400	Weak transcription	HMEC	breast
8	chr3:195022800-195073400	Weak transcription	NHEK	skin
9	chr3:195025400-195050600	Weak transcription	HSMMtube	muscle
10	chr3:195026800-195051400	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr3:195029200-195046800	Weak transcription	NHDF-Ad	bronchial
12	chr3:195033000-195046800	Weak transcription	HSMM	muscle
13	chr3:195033800-195045800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:195034800-195076800	Weak transcription	Psoas Muscle	Psoas
15	chr3:195039200-195043200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr3:195040200-195046400	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr3:195040400-195043400	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr3:195040400-195047000	Weak transcription	Spleen	Spleen
19	chr3:195040400-195049200	Weak transcription	HUVEC	blood vessel
20	chr3:195040400-195051400	Weak transcription	NH-A	brain
21	chr3:195040400-195051800	Weak transcription	Right Ventricle	heart
22	chr3:195040400-195053000	Weak transcription	A549	lung
23	chr3:195040400-195062600	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr3:195040400-195064800	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr3:195040400-195066000	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr3:195040400-195076400	Weak transcription	Brain Cingulate Gyrus	brain
27	chr3:195040400-195076600	Weak transcription	Brain Anterior Caudate	brain
28	chr3:195040400-195079400	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr3:195040400-195108400	Weak transcription	Colonic Mucosa	Colon
30	chr3:195040600-195047000	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr3:195040600-195051200	Weak transcription	HepG2	liver
32	chr3:195040600-195059000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr3:195040600-195111200	Weak transcription	Fetal Brain Male	brain
34	chr3:195040800-195043200	Strong transcription	Fetal Thymus	thymus
35	chr3:195040800-195047000	Weak transcription	Ovary	ovary
36	chr3:195040800-195048800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:195040800-195051600	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr3:195040800-195071200	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr3:195040800-195072800	Weak transcription	K562	blood
40	chr3:195040800-195073200	Weak transcription	Pancreas	Pancrea
41	chr3:195040800-195076400	Weak transcription	Brain Hippocampus Middle	brain
42	chr3:195041000-195044000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr3:195041000-195047000	Weak transcription	Fetal Intestine Large	intestine
44	chr3:195041000-195047200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr3:195041000-195048000	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr3:195041000-195050000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr3:195041000-195050200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr3:195041000-195050200	Weak transcription	Fetal Muscle Trunk	muscle
49	chr3:195041000-195050400	Weak transcription	Stomach Smooth Muscle	stomach
50	chr3:195041000-195051400	Weak transcription	Esophagus	oesophagus

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