Variant report

Variant	rs6816002
Chromosome Location	chr4:152589439-152589440
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: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10001603	0.86[EUR][1000 genomes]
rs10013612	0.82[EUR][1000 genomes]
rs10016160	0.82[EUR][1000 genomes]
rs10019048	0.89[GIH][hapmap]
rs10222838	0.82[EUR][1000 genomes]
rs10222925	0.82[EUR][1000 genomes]
rs11723227	0.82[EUR][1000 genomes]
rs12503677	0.93[EUR][1000 genomes]
rs12641433	0.96[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12641438	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12641441	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12647420	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12647462	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12647465	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12647616	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1366907	0.92[CEU][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs1397683	0.88[CEU][hapmap]
rs1429558	0.82[EUR][1000 genomes]
rs1429559	0.92[CEU][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs17360371	0.80[EUR][1000 genomes]
rs17360385	0.84[EUR][1000 genomes]
rs1877185	0.82[EUR][1000 genomes]
rs1877186	0.82[EUR][1000 genomes]
rs1877187	0.85[GIH][hapmap]
rs1877188	0.88[CEU][hapmap];0.91[CHB][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1896883	0.89[GIH][hapmap]
rs2089811	0.92[CEU][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs2175409	0.82[EUR][1000 genomes]
rs2278304	0.89[GIH][hapmap]
rs2406973	0.96[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2406974	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2840130	0.89[GIH][hapmap];0.82[MEX][hapmap]
rs28659854	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3805356	0.92[CEU][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs3828546	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs4571	0.87[GIH][hapmap]
rs4696106	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4696107	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4696108	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4696110	0.84[EUR][1000 genomes]
rs4696285	0.85[GIH][hapmap]
rs4696286	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4696287	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4696290	0.96[CEU][hapmap];0.82[GIH][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes]
rs4696295	0.88[CEU][hapmap];0.85[TSI][hapmap]
rs58751443	0.81[EUR][1000 genomes]
rs59350867	0.82[EUR][1000 genomes]
rs6535816	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs6535822	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs6810860	0.89[GIH][hapmap]
rs6833368	0.89[GIH][hapmap]
rs6834095	0.89[GIH][hapmap]
rs6838966	0.89[GIH][hapmap]
rs6839074	0.89[GIH][hapmap]
rs6840360	0.89[GIH][hapmap]
rs6840678	0.87[GIH][hapmap]
rs6847844	0.82[EUR][1000 genomes]
rs6849050	0.89[GIH][hapmap]
rs6849111	0.81[EUR][1000 genomes]
rs6855883	0.82[EUR][1000 genomes]
rs6857073	0.82[EUR][1000 genomes]
rs7439465	0.89[GIH][hapmap]
rs7654294	0.82[EUR][1000 genomes]
rs7669465	0.96[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7669761	0.96[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7675818	0.82[EUR][1000 genomes]
rs9996320	0.93[EUR][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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6816002	PET112L	cis	multi-tissue	Pritchard

Chromatin state (count:76 , 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	chr4:152583600-152589600	Weak transcription	Fetal Brain Female	brain
25	chr4:152583800-152595200	Weak transcription	Esophagus	oesophagus
26	chr4:152584600-152589800	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr4:152584600-152595400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr4:152584800-152595800	Weak transcription	Fetal Intestine Large	intestine
29	chr4:152585000-152590000	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr4:152585200-152596000	Weak transcription	Colonic Mucosa	Colon
31	chr4:152585600-152592000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr4:152585600-152594400	Weak transcription	Fetal Stomach	stomach
33	chr4:152585600-152594800	Weak transcription	Ovary	ovary
34	chr4:152585600-152628600	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr4:152585800-152589800	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr4:152585800-152591800	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr4:152585800-152592000	Weak transcription	Fetal Intestine Small	intestine
38	chr4:152585800-152592600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr4:152585800-152595000	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr4:152585800-152595200	Weak transcription	Duodenum Mucosa	Duodenum
41	chr4:152585800-152596200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr4:152585800-152600400	Weak transcription	Gastric	stomach
43	chr4:152585800-152640400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr4:152586000-152596600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr4:152586400-152590800	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr4:152586400-152609000	Weak transcription	Primary hematopoietic stem cells	blood
47	chr4:152586600-152590800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr4:152586600-152592000	Weak transcription	Left Ventricle	heart
49	chr4:152586600-152593200	Enhancers	Skeletal Muscle Male	skeletal muscle
50	chr4:152586600-152595200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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