Variant report

Variant	rs1586660
Chromosome Location	chr1:212266531-212266532
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:212265510..212267948-chr1:212458741..212460334,2	K562	blood:
2	chr1:212260403..212263243-chr1:212265417..212267031,2	K562	blood:
3	chr1:212255227..212257947-chr1:212264882..212267056,2	K562	blood:

Variant related genes	Relation type
ENSG00000066027	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10863938	0.90[GIH][hapmap];1.00[TSI][hapmap]
rs2358439	0.82[AFR][1000 genomes]
rs2788130	0.90[GIH][hapmap];1.00[TSI][hapmap]
rs2788135	0.90[GIH][hapmap];1.00[TSI][hapmap]
rs2788137	0.90[GIH][hapmap];1.00[TSI][hapmap]
rs2788138	1.00[CEU][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes]
rs2788141	0.90[GIH][hapmap];1.00[TSI][hapmap]
rs2808380	0.90[GIH][hapmap];1.00[TSI][hapmap]
rs2808388	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap]
rs2970586	0.90[GIH][hapmap];1.00[TSI][hapmap]
rs2970604	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2993524	0.88[TSI][hapmap]
rs2993535	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap]
rs2993536	1.00[TSI][hapmap]
rs2993538	0.83[AFR][1000 genomes]
rs2993540	0.90[GIH][hapmap];1.00[TSI][hapmap]
rs2993545	1.00[AMR][1000 genomes]
rs2993546	0.90[GIH][hapmap];1.00[TSI][hapmap]
rs3009986	0.90[GIH][hapmap];1.00[TSI][hapmap]
rs3009991	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3009994	0.90[GIH][hapmap];0.90[TSI][hapmap]
rs3009997	0.87[AMR][1000 genomes]
rs3010008	0.90[GIH][hapmap];1.00[TSI][hapmap]
rs3010014	0.88[GIH][hapmap];1.00[TSI][hapmap]
rs3010016	0.97[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3010022	0.90[GIH][hapmap];1.00[TSI][hapmap]
rs3010029	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4951436	0.96[EUR][1000 genomes]
rs6675701	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6690508	1.00[EUR][1000 genomes]
rs7520161	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7535988	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7545292	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][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	nsv999738	chr1:212218618-212513690	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1586660	LPGAT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212214400-212278000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:212229600-212266600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:212234200-212267400	Strong transcription	Dnd41	blood
4	chr1:212237200-212267000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
5	chr1:212237600-212266800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr1:212241600-212284600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr1:212244600-212267200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:212253000-212270800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr1:212254800-212278000	Weak transcription	NHDF-Ad	bronchial
10	chr1:212256000-212266600	Weak transcription	Fetal Muscle Trunk	muscle
11	chr1:212256000-212266800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr1:212256000-212271000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr1:212256400-212271200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr1:212256400-212278600	Weak transcription	NHLF	lung
15	chr1:212261800-212271800	Weak transcription	Spleen	Spleen
16	chr1:212262000-212266600	Weak transcription	HSMM	muscle
17	chr1:212262000-212266800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr1:212262000-212271800	Weak transcription	Hela-S3	cervix
19	chr1:212262000-212276800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr1:212262000-212283000	Weak transcription	NH-A	brain
21	chr1:212262000-212284400	Weak transcription	Osteobl	bone
22	chr1:212262200-212266600	Weak transcription	Thymus	Thymus
23	chr1:212262200-212272200	Weak transcription	Gastric	stomach
24	chr1:212262200-212273600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:212262200-212273800	Weak transcription	NHEK	skin
26	chr1:212262200-212279600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr1:212262200-212289200	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr1:212262600-212267200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr1:212262600-212267800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr1:212262600-212273800	Weak transcription	HMEC	breast
31	chr1:212263000-212275200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr1:212263400-212267200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr1:212263400-212268200	Weak transcription	Right Atrium	heart
34	chr1:212263400-212268400	Strong transcription	Fetal Thymus	thymus
35	chr1:212263400-212271600	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr1:212263400-212274000	Weak transcription	Fetal Lung	lung
37	chr1:212263400-212278200	Weak transcription	Duodenum Mucosa	Duodenum
38	chr1:212263600-212269800	Weak transcription	Primary T cells from cord blood	blood
39	chr1:212263600-212270200	Weak transcription	Primary hematopoietic stem cells	blood
40	chr1:212263600-212273800	Weak transcription	HUVEC	blood vessel
41	chr1:212264000-212273800	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr1:212264400-212268200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr1:212264400-212282400	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr1:212264800-212268400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr1:212265000-212268000	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr1:212265000-212268800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr1:212265000-212270400	Weak transcription	GM12878-XiMat	blood
48	chr1:212265200-212266800	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr1:212265200-212269800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr1:212265200-212270200	Weak transcription	HUES64 Cell Line	embryonic stem cell

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