Variant report

Variant	rs28454065
Chromosome Location	chr4:152589913-152589914
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAM160A1-1	chr4:152588607-152590955	XLOC_003734

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10002512	1.00[AMR][1000 genomes]
rs10002750	1.00[AMR][1000 genomes]
rs10010061	1.00[AMR][1000 genomes]
rs10014639	1.00[AMR][1000 genomes]
rs10015816	1.00[AMR][1000 genomes]
rs10017489	1.00[AMR][1000 genomes]
rs10020313	1.00[AMR][1000 genomes]
rs10027105	1.00[AMR][1000 genomes]
rs10032584	1.00[AMR][1000 genomes]
rs10034746	1.00[AMR][1000 genomes]
rs10212987	1.00[AMR][1000 genomes]
rs10213361	1.00[AMR][1000 genomes]
rs10471071	1.00[AMR][1000 genomes]
rs10471072	1.00[AMR][1000 genomes]
rs13353741	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13435896	1.00[AMR][1000 genomes]
rs17027675	1.00[AMR][1000 genomes]
rs17027703	1.00[AMR][1000 genomes]
rs17027710	1.00[AMR][1000 genomes]
rs17027725	1.00[AMR][1000 genomes]
rs17027738	1.00[AMR][1000 genomes]
rs17027739	1.00[AMR][1000 genomes]
rs17027742	1.00[AMR][1000 genomes]
rs17027757	1.00[AMR][1000 genomes]
rs17027762	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17027764	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17027767	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28404927	1.00[AMR][1000 genomes]
rs28417352	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28461656	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28494961	1.00[AMR][1000 genomes]
rs28539581	1.00[AMR][1000 genomes]
rs28540596	1.00[AMR][1000 genomes]
rs28558989	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28591074	1.00[AMR][1000 genomes]
rs28595853	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28618192	1.00[AMR][1000 genomes]
rs28634312	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28656459	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28722860	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28788179	1.00[AMR][1000 genomes]
rs28798801	1.00[AMR][1000 genomes]
rs28822494	1.00[AMR][1000 genomes]
rs28837860	1.00[AMR][1000 genomes]
rs28884810	1.00[AMR][1000 genomes]
rs57562339	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61653326	1.00[AMR][1000 genomes]
rs72954810	1.00[AMR][1000 genomes]
rs72954898	1.00[AMR][1000 genomes]
rs72956911	1.00[AMR][1000 genomes]
rs72956926	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72956927	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9307882	1.00[AMR][1000 genomes]
rs9307883	1.00[AMR][1000 genomes]
rs9307884	1.00[AMR][1000 genomes]
rs9307885	1.00[AMR][1000 genomes]
rs9683731	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9994720	1.00[AMR][1000 genomes]
rs9997778	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2755535	chr4:152549395-152609395	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv4551	chr4:152582617-152627367	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152563800-152625200	Weak transcription	Hela-S3	cervix
2	chr4:152564200-152595200	Weak transcription	Aorta	Aorta
3	chr4:152567400-152608600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr4:152567800-152609000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr4:152571600-152595000	Weak transcription	HepG2	liver
6	chr4:152578400-152595200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr4:152579200-152597400	Weak transcription	Liver	Liver
8	chr4:152579600-152592200	Weak transcription	Right Ventricle	heart
9	chr4:152579800-152592800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr4:152580000-152595200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr4:152580200-152596000	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr4:152580800-152595800	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr4:152580800-152596800	Weak transcription	Primary T cells from cord blood	blood
14	chr4:152581000-152592000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr4:152581200-152602800	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr4:152581200-152608400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr4:152581600-152595000	Weak transcription	Stomach Smooth Muscle	stomach
18	chr4:152581800-152595600	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr4:152582400-152592600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr4:152582400-152595000	Weak transcription	Lung	lung
21	chr4:152582400-152595800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr4:152583000-152591800	Weak transcription	Adipose Nuclei	Adipose
23	chr4:152583200-152596000	Weak transcription	Spleen	Spleen
24	chr4:152583800-152595200	Weak transcription	Esophagus	oesophagus
25	chr4:152584600-152595400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr4:152584800-152595800	Weak transcription	Fetal Intestine Large	intestine
27	chr4:152585000-152590000	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr4:152585200-152596000	Weak transcription	Colonic Mucosa	Colon
29	chr4:152585600-152592000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr4:152585600-152594400	Weak transcription	Fetal Stomach	stomach
31	chr4:152585600-152594800	Weak transcription	Ovary	ovary
32	chr4:152585600-152628600	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr4:152585800-152591800	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr4:152585800-152592000	Weak transcription	Fetal Intestine Small	intestine
35	chr4:152585800-152592600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr4:152585800-152595000	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr4:152585800-152595200	Weak transcription	Duodenum Mucosa	Duodenum
38	chr4:152585800-152596200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr4:152585800-152600400	Weak transcription	Gastric	stomach
40	chr4:152585800-152640400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr4:152586000-152596600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr4:152586400-152590800	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr4:152586400-152609000	Weak transcription	Primary hematopoietic stem cells	blood
44	chr4:152586600-152590800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr4:152586600-152592000	Weak transcription	Left Ventricle	heart
46	chr4:152586600-152593200	Enhancers	Skeletal Muscle Male	skeletal muscle
47	chr4:152586600-152595200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr4:152586800-152591000	Weak transcription	Pancreas	Pancrea
49	chr4:152587800-152590200	Enhancers	Fetal Thymus	thymus
50	chr4:152587800-152595200	Weak transcription	Fetal Brain Male	brain

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