Variant report

Variant	rs2239817
Chromosome Location	chr1:172524788-172524789
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:172524779..172527328-chr1:172528773..172530813,3	K562	blood:
2	chr1:172417892..172422705-chr1:172522786..172525518,5	MCF-7	breast:
3	chr1:172500340..172502764-chr1:172523653..172526492,2	K562	blood:
4	chr1:172518787..172521238-chr1:172523963..172525755,2	MCF-7	breast:
5	chr1:172524779..172527801-chr1:172528773..172532155,3	K562	blood:
6	chr1:172518503..172521143-chr1:172524413..172526637,2	K562	blood:

Variant related genes	Relation type
ENSG00000094975	Chromatin interaction
ENSG00000180999	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10157501	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10752995	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10911830	0.88[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10911833	0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10911843	0.91[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10911859	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10911862	0.91[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10911875	1.00[ASN][1000 genomes]
rs10911920	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10912009	0.87[EUR][1000 genomes]
rs10912075	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1159378	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12021702	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12025433	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12038654	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12041837	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12070393	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12073872	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12093274	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12118647	0.81[ASN][1000 genomes]
rs12120798	1.00[CHB][hapmap];0.88[JPT][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12123755	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12130435	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12145007	0.81[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2239816	0.91[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2285143	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2285664	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2472549	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3738736	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3754426	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3830150	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6424954	0.82[ASN][1000 genomes]
rs6424955	0.88[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6424956	0.81[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6424965	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6657023	0.83[ASN][1000 genomes]
rs6679222	0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6688929	0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6691320	0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6691528	0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6694111	0.82[ASN][1000 genomes]
rs6697618	0.82[ASN][1000 genomes]
rs6698031	0.82[ASN][1000 genomes]
rs6699802	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6702420	0.81[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs72710417	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7514814	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7517856	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7519911	0.80[ASN][1000 genomes]
rs7532580	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7542003	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7553020	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9943237	0.91[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.83[TSI][hapmap];0.83[ASN][1000 genomes]
rs9970543	0.80[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	nsv872547	chr1:172511969-172545832	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv872548	chr1:172518012-172551724	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2239817	FMO2	cis	cerebellum	SCAN
rs2239817	SUCO	cis	lung	GTEx
rs2239817	FMO1	cis	parietal	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172503400-172528600	Weak transcription	Aorta	Aorta
2	chr1:172503400-172528600	Weak transcription	Lung	lung
3	chr1:172503600-172531600	Weak transcription	Esophagus	oesophagus
4	chr1:172503800-172529000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr1:172503800-172534200	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr1:172504200-172527000	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr1:172506000-172532600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr1:172506200-172525000	Weak transcription	Duodenum Mucosa	Duodenum
9	chr1:172506200-172526200	Weak transcription	Fetal Intestine Large	intestine
10	chr1:172506200-172528400	Weak transcription	Fetal Stomach	stomach
11	chr1:172507400-172526400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr1:172507400-172528600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:172508200-172526400	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr1:172509400-172530800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr1:172510000-172525000	Weak transcription	Left Ventricle	heart
16	chr1:172511800-172524800	Weak transcription	Liver	Liver
17	chr1:172511800-172528600	Weak transcription	Stomach Smooth Muscle	stomach
18	chr1:172511800-172557800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr1:172512000-172529000	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr1:172512000-172534200	Weak transcription	Gastric	stomach
21	chr1:172513800-172525000	Weak transcription	Fetal Thymus	thymus
22	chr1:172514200-172558800	Weak transcription	Small Intestine	intestine
23	chr1:172514400-172526200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr1:172514800-172528600	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr1:172514800-172530200	Weak transcription	Thymus	Thymus
26	chr1:172515200-172524800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr1:172515200-172525200	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr1:172515200-172528000	Weak transcription	Rectal Smooth Muscle	rectum
29	chr1:172515200-172528200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr1:172515400-172528600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr1:172516000-172532800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr1:172516200-172528800	Weak transcription	Pancreas	Pancrea
33	chr1:172516400-172526400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr1:172516400-172527400	Weak transcription	NHLF	lung
35	chr1:172516600-172528800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr1:172516800-172550200	Weak transcription	Fetal Heart	heart
37	chr1:172517800-172527200	Weak transcription	Fetal Kidney	kidney
38	chr1:172518000-172529000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr1:172518600-172533000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr1:172518800-172525000	Weak transcription	HepG2	liver
41	chr1:172519000-172525600	Weak transcription	Fetal Brain Female	brain
42	chr1:172519000-172530000	Weak transcription	NH-A	brain
43	chr1:172519000-172530200	Weak transcription	Brain Substantia Nigra	brain
44	chr1:172519200-172526800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr1:172519200-172526800	Weak transcription	A549	lung
46	chr1:172519200-172527200	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr1:172519200-172528000	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr1:172519200-172529000	Weak transcription	Brain Germinal Matrix	brain
49	chr1:172519200-172534600	Weak transcription	Right Ventricle	heart
50	chr1:172519200-172559000	Weak transcription	Psoas Muscle	Psoas

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