Variant report

Variant	rs10089
Chromosome Location	chr5:127522543-127522544
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC27A6-1	chr5:127522490-127522778	NONHSAT103660

Extended variants
information (count: 80 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10057122	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10059867	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10060181	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10060390	1.00[CEU][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10061367	1.00[CEU][hapmap];0.91[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10064357	0.83[EUR][1000 genomes]
rs10223203	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10223313	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10463838	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10463839	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10478796	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10478798	1.00[CEU][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes]
rs10478803	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11957052	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13355233	1.00[CEU][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.96[TSI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13356473	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13357268	1.00[CEU][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.96[TSI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1432614	0.95[CEU][hapmap];0.95[JPT][hapmap]
rs1432615	0.95[CEU][hapmap];0.91[JPT][hapmap]
rs1559263	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1560636	1.00[CEU][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17164310	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17164395	1.00[YRI][hapmap]
rs17164427	0.95[CEU][hapmap];0.94[CHD][hapmap];0.91[JPT][hapmap];0.92[TSI][hapmap]
rs17764954	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17839658	1.00[YRI][hapmap]
rs1842006	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1864922	1.00[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.96[TSI][hapmap];0.83[EUR][1000 genomes]
rs1864923	1.00[CEU][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes]
rs1962291	1.00[CEU][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.96[TSI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2016015	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2054444	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2228112	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2409109	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2898096	1.00[CEU][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes]
rs3087889	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3792866	1.00[CEU][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3805603	0.82[YRI][hapmap]
rs3805606	1.00[CEU][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3805607	1.00[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.96[TSI][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3805612	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3805615	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3805616	0.82[JPT][hapmap]
rs3816006	1.00[CEU][hapmap];0.91[JPT][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4835941	1.00[CEU][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4835943	1.00[CEU][hapmap];0.91[JPT][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4835944	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4835945	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4836360	1.00[CEU][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4836361	1.00[CEU][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4836363	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4836366	1.00[CEU][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4836367	1.00[CEU][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4836368	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4836369	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4836370	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56066100	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57249773	0.83[AFR][1000 genomes]
rs59484271	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6595806	1.00[CEU][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6595807	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6862701	0.95[CEU][hapmap];0.86[JPT][hapmap]
rs6873339	0.95[CEU][hapmap];0.95[JPT][hapmap]
rs6875982	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6887674	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6887847	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72794379	0.80[AFR][1000 genomes]
rs72794386	0.86[AFR][1000 genomes]
rs72794392	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72794396	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72794400	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72794401	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs736969	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7703634	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7713860	1.00[CEU][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7718286	1.00[CEU][hapmap];0.91[JPT][hapmap];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs883074	0.90[CEU][hapmap];0.86[JPT][hapmap]
rs891886	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9968597	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830482	chr5:127475398-127665377	Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Ileal carcinoids	21139019	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10089	FBN2	cis	parietal	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:127441200-127536800	Weak transcription	Colonic Mucosa	Colon
2	chr5:127442400-127525000	Weak transcription	Right Ventricle	heart
3	chr5:127447000-127525000	Weak transcription	Fetal Brain Male	brain
4	chr5:127453600-127525400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr5:127457600-127534400	Weak transcription	Pancreas	Pancrea
6	chr5:127460800-127525200	Weak transcription	Spleen	Spleen
7	chr5:127463200-127533000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr5:127465400-127532200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr5:127467600-127525000	Weak transcription	Thymus	Thymus
10	chr5:127468000-127536800	Weak transcription	Fetal Brain Female	brain
11	chr5:127469200-127524200	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr5:127478400-127524600	Weak transcription	Small Intestine	intestine
13	chr5:127478600-127531600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr5:127479200-127532200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr5:127480600-127532400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr5:127480600-127534400	Weak transcription	Gastric	stomach
17	chr5:127485000-127536800	Weak transcription	Colon Smooth Muscle	Colon
18	chr5:127488600-127533200	Weak transcription	Stomach Mucosa	stomach
19	chr5:127488800-127523600	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr5:127490400-127532800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr5:127490800-127529200	Weak transcription	Aorta	Aorta
22	chr5:127490800-127536600	Weak transcription	Brain Cingulate Gyrus	brain
23	chr5:127492200-127527200	Weak transcription	NHDF-Ad	bronchial
24	chr5:127493200-127529200	Weak transcription	Psoas Muscle	Psoas
25	chr5:127494400-127526800	Weak transcription	Fetal Lung	lung
26	chr5:127494400-127534800	Weak transcription	Liver	Liver
27	chr5:127494400-127536800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr5:127494600-127534400	Weak transcription	HUVEC	blood vessel
29	chr5:127496600-127525800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr5:127498400-127532200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr5:127499000-127532400	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr5:127499000-127533400	Weak transcription	GM12878-XiMat	blood
33	chr5:127499200-127534600	Weak transcription	Lung	lung
34	chr5:127499400-127528400	Weak transcription	Fetal Intestine Small	intestine
35	chr5:127500400-127532400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr5:127500400-127536800	Weak transcription	NHEK	skin
37	chr5:127504600-127536800	Weak transcription	Rectal Smooth Muscle	rectum
38	chr5:127508400-127533200	Weak transcription	A549	lung
39	chr5:127510000-127532600	Weak transcription	Fetal Heart	heart
40	chr5:127511000-127524200	Weak transcription	Osteobl	bone
41	chr5:127511000-127532400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr5:127511400-127535000	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr5:127513000-127529200	Strong transcription	Duodenum Mucosa	Duodenum
44	chr5:127513200-127523200	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr5:127514000-127529200	Weak transcription	HSMMtube	muscle
46	chr5:127514200-127522600	Strong transcription	Skeletal Muscle Female	skeletal muscle
47	chr5:127514400-127522600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr5:127514400-127533000	Weak transcription	NHLF	lung
49	chr5:127514600-127523000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr5:127514800-127522800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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