Variant report

Variant	rs1962291
Chromosome Location	chr5:127445373-127445374
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:127417788..127421083-chr5:127443681..127446699,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC27A6-2	chr5:127445178-127446686	NONHSAT103657

Variant related genes	Relation type
ENSG00000064651	Chromatin interaction
ENSG00000245937	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10045113	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10045307	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10059867	0.83[ASN][1000 genomes]
rs10060181	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10060390	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10061367	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10064098	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10064357	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10089	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]
rs1012851	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10223203	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1036171	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10463838	1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10463839	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10478796	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10478798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10478803	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10519973	0.84[CHB][hapmap]
rs10519974	0.84[CHB][hapmap]
rs11957052	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13355233	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13356473	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13357268	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13358455	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1368270	0.89[CHB][hapmap]
rs1432614	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1432615	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1559263	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.96[TSI][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1560636	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17164310	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17164427	0.95[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17764954	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1842006	1.00[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1864922	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1864923	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1985268	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2016015	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2054444	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2190797	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2228112	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2409109	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2898096	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3087889	1.00[CEU][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35212223	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3792866	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3805604	0.84[CHB][hapmap]
rs3805606	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3805607	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.90[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3805612	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3805615	1.00[CEU][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3816006	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4835940	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4835941	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4835942	0.84[CHB][hapmap];0.87[MEX][hapmap]
rs4835943	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4835944	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4835945	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4836358	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4836359	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4836360	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4836361	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4836362	0.84[CHB][hapmap]
rs4836363	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4836365	0.84[CHB][hapmap]
rs4836366	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4836367	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4836368	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4836369	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4836370	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56066100	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58433932	0.86[AMR][1000 genomes]
rs60964984	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62373701	0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6595798	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6595800	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6595806	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6595807	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6862701	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6873339	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6875982	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6879970	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6887674	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6887847	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72794392	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72794396	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72794400	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72794401	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs736969	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs758179	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7703634	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7713860	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7718286	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7732599	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs883074	0.90[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap]
rs891886	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9968597	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][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	nsv4993	chr5:127405214-127445622	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	esv1825644	chr5:127427533-127450581	Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1962291	FBN2	cis	parietal	SCAN

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:127421400-127450200	Weak transcription	Fetal Thymus	thymus
2	chr5:127421600-127466800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr5:127423600-127494000	Weak transcription	K562	blood
4	chr5:127432400-127454600	Weak transcription	Fetal Kidney	kidney
5	chr5:127434400-127449000	Weak transcription	Dnd41	blood
6	chr5:127434800-127445400	Weak transcription	Primary T cells from cord blood	blood
7	chr5:127434800-127450600	Weak transcription	Fetal Intestine Small	intestine
8	chr5:127435000-127445800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr5:127435000-127447600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr5:127435000-127447600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr5:127435000-127448600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr5:127435000-127448600	Weak transcription	Primary hematopoietic stem cells	blood
13	chr5:127435000-127449600	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr5:127435200-127450400	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr5:127435200-127450800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr5:127435600-127445600	Weak transcription	Primary B cells from cord blood	blood
17	chr5:127435600-127449400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr5:127437000-127449800	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr5:127437200-127449800	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr5:127437400-127446000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr5:127437600-127447600	Weak transcription	Brain Anterior Caudate	brain
22	chr5:127437600-127447600	Weak transcription	NH-A	brain
23	chr5:127437800-127451600	Weak transcription	HMEC	breast
24	chr5:127438000-127450600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr5:127438400-127450200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr5:127439400-127447600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr5:127439400-127450400	Weak transcription	Brain Cingulate Gyrus	brain
28	chr5:127441200-127450600	Weak transcription	Aorta	Aorta
29	chr5:127441200-127536800	Weak transcription	Colonic Mucosa	Colon
30	chr5:127441400-127445400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr5:127441400-127445800	Weak transcription	A549	lung
32	chr5:127441400-127449600	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr5:127441400-127450600	Weak transcription	Ovary	ovary
34	chr5:127441400-127450600	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr5:127441400-127457400	Weak transcription	Stomach Mucosa	stomach
36	chr5:127441600-127450600	Weak transcription	Brain Hippocampus Middle	brain
37	chr5:127441600-127450600	Weak transcription	Stomach Smooth Muscle	stomach
38	chr5:127441800-127445400	Weak transcription	Brain Angular Gyrus	brain
39	chr5:127441800-127448400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr5:127441800-127450600	Weak transcription	Rectal Smooth Muscle	rectum
41	chr5:127441800-127451000	Weak transcription	Colon Smooth Muscle	Colon
42	chr5:127442000-127449600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr5:127442400-127525000	Weak transcription	Right Ventricle	heart
44	chr5:127442800-127448800	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr5:127443000-127457200	Weak transcription	Pancreas	Pancrea
46	chr5:127443000-127467000	Weak transcription	Esophagus	oesophagus
47	chr5:127443600-127450200	Weak transcription	Adipose Nuclei	Adipose
48	chr5:127443600-127450600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr5:127443800-127459800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr5:127444000-127446800	Strong transcription	Fetal Intestine Large	intestine

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