Variant report

Variant	rs12038654
Chromosome Location	chr1:172582070-172582071
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	chr1:172577180..172579223-chr1:172580672..172583395,2	K562	blood:

Variant related genes	Relation type
ENSG00000094975	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10157501	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10752995	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10911830	0.81[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap]
rs10911833	0.94[JPT][hapmap]
rs10911843	0.91[CEU][hapmap];0.87[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap]
rs10911859	0.80[AMR][1000 genomes]
rs10911862	0.91[CEU][hapmap];0.87[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes]
rs10911920	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10912009	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10912075	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1159378	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12021702	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12025433	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12041837	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12070393	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12073872	0.95[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12093274	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12120798	0.94[CHB][hapmap];0.81[JPT][hapmap];0.88[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12123755	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12130435	0.80[AMR][1000 genomes]
rs12145007	0.92[JPT][hapmap]
rs2239816	0.91[CEU][hapmap];0.87[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap];0.80[AMR][1000 genomes]
rs2239817	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2285143	0.80[AMR][1000 genomes]
rs2285664	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2472549	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3738736	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3754426	0.91[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.89[AMR][1000 genomes]
rs3830150	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6424955	0.81[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap]
rs6424956	0.90[CHD][hapmap];0.94[JPT][hapmap]
rs6424965	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6679222	0.93[JPT][hapmap]
rs6688929	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs6691320	0.94[JPT][hapmap]
rs6691528	0.93[JPT][hapmap]
rs6699802	0.94[JPT][hapmap]
rs6702420	1.00[JPT][hapmap]
rs72710417	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7514814	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7519911	0.90[ASN][1000 genomes]
rs7532580	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7542003	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7553020	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9943237	0.91[CEU][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];0.83[TSI][hapmap]
rs9970543	0.90[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12038654	SUCO	cis	lung	GTEx
rs12038654	FMO2	cis	cerebellum	SCAN
rs12038654	FMO1	cis	parietal	SCAN

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172559000-172583400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:172560000-172582400	Weak transcription	Brain Substantia Nigra	brain
3	chr1:172566600-172582200	Weak transcription	Fetal Intestine Small	intestine
4	chr1:172566600-172595800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr1:172567400-172582200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr1:172570600-172584000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr1:172570600-172585400	Weak transcription	Aorta	Aorta
8	chr1:172573400-172582400	Weak transcription	Stomach Smooth Muscle	stomach
9	chr1:172576800-172585400	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr1:172578800-172582600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr1:172579400-172585400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:172579600-172585200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr1:172579800-172582400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr1:172579800-172588600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr1:172580000-172582200	Weak transcription	Fetal Muscle Leg	muscle
16	chr1:172580000-172582200	Weak transcription	NHLF	lung
17	chr1:172580000-172582200	Weak transcription	Osteobl	bone
18	chr1:172580000-172583000	Weak transcription	GM12878-XiMat	blood
19	chr1:172580000-172583800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr1:172580000-172584200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr1:172580000-172584400	Weak transcription	HSMMtube	muscle
22	chr1:172580000-172585400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr1:172580200-172582400	Weak transcription	Fetal Muscle Trunk	muscle
24	chr1:172580200-172585000	Weak transcription	Duodenum Mucosa	Duodenum
25	chr1:172580200-172589800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr1:172580400-172582200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr1:172580400-172582200	Weak transcription	Brain Anterior Caudate	brain
28	chr1:172580400-172582400	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr1:172580400-172582800	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr1:172580400-172584000	Weak transcription	Dnd41	blood
31	chr1:172580600-172582400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr1:172580600-172582400	Weak transcription	HSMM	muscle
33	chr1:172580600-172582400	Weak transcription	HUVEC	blood vessel
34	chr1:172580600-172582600	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr1:172580600-172582600	Weak transcription	Fetal Brain Female	brain
36	chr1:172580600-172583000	Weak transcription	Liver	Liver
37	chr1:172580600-172583000	Weak transcription	HepG2	liver
38	chr1:172580600-172583600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr1:172580600-172585400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr1:172580800-172582400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr1:172580800-172582400	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr1:172580800-172583200	Weak transcription	Fetal Thymus	thymus
43	chr1:172580800-172583600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr1:172580800-172583600	Weak transcription	Adipose Nuclei	Adipose
45	chr1:172580800-172583800	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr1:172580800-172583800	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr1:172580800-172585000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr1:172580800-172585400	Weak transcription	Placenta	Placenta
49	chr1:172580800-172588800	Weak transcription	NH-A	brain
50	chr1:172581000-172582800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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