Variant report

Variant	rs7544583
Chromosome Location	chr1:173688388-173688389
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:173686308..173688392-chr1:173689930..173692042,2	K562	blood:
2	chr1:173686890..173689888-chr1:173826040..173828331,2	MCF-7	breast:
3	chr1:173679457..173681127-chr1:173688388..173689983,2	MCF-7	breast:
4	chr1:173685811..173687806-chr1:173687936..173689496,2	K562	blood:
5	chr1:173687895..173689585-chr1:173692482..173695234,2	MCF-7	breast:
6	chr1:173680023..173685703-chr1:173685874..173692365,9	K562	blood:

Variant related genes	Relation type
ENSG00000076321	Chromatin interaction

Extended variants
information (count: 101 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10081990	0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10158663	1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10399912	0.86[YRI][hapmap]
rs10798298	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs10912677	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10912678	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10912680	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10912682	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10912684	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs1115487	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs11487392	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12065033	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12067571	1.00[EUR][1000 genomes]
rs12070556	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs12073601	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12074150	1.00[EUR][1000 genomes]
rs12080389	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12082206	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs12083423	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12085748	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs12085894	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs12089398	1.00[MEX][hapmap]
rs12094130	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12095090	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12096832	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs12098124	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1322771	1.00[ASW][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs1322772	1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs13375555	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1474907	1.00[ASW][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs16846278	1.00[MEX][hapmap]
rs16846383	1.00[ASW][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs16846395	1.00[ASW][hapmap];0.82[YRI][hapmap]
rs16846398	1.00[ASW][hapmap];0.86[YRI][hapmap]
rs16846420	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs2224657	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs28578576	1.00[ASW][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];0.82[AMR][1000 genomes]
rs4652283	0.90[MKK][hapmap]
rs4652298	0.90[MKK][hapmap]
rs4652328	0.83[MKK][hapmap]
rs59845733	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs6425256	1.00[ASW][hapmap];0.82[YRI][hapmap]
rs6425257	1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6658217	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6663880	1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6670574	1.00[EUR][1000 genomes]
rs6675762	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs6686455	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs6689764	0.88[AMR][1000 genomes]
rs6691327	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs6691922	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs6692452	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs6695782	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs6698348	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs6702485	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7518130	1.00[ASW][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.82[AMR][1000 genomes]
rs7522788	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs7534521	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs7536773	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs7550036	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7552840	1.00[ASW][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];0.88[AMR][1000 genomes]
rs9282959	1.00[ASW][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9282960	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9286886	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9286887	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9286890	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9286894	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9425413	0.82[YRI][hapmap]
rs9425414	1.00[ASW][hapmap];0.82[YRI][hapmap]
rs9425415	1.00[ASW][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];0.88[AMR][1000 genomes]
rs9425418	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9425419	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9425420	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9425421	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9425422	1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9425423	1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9425424	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9425425	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9425426	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9425431	0.90[MKK][hapmap]
rs9425433	0.85[MKK][hapmap]
rs9425734	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9425736	1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9425738	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9425740	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9425741	1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9425742	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9425746	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9425747	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9425750	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9425751	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9425752	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9425758	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9425759	1.00[ASW][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.82[AMR][1000 genomes]
rs9425761	1.00[ASW][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9425768	1.00[ASW][hapmap]
rs9442660	1.00[ASW][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9970488	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9970633	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][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	nsv1012384	chr1:173614816-173974426	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	294 gene(s)	inside rSNPs	diseases
2	nsv1014827	chr1:173653453-173692470	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7544583	OR9I1	trans	lymphoblastoid	seeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173684800-173695000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:173684800-173702800	Weak transcription	Spleen	Spleen
3	chr1:173685000-173695200	Weak transcription	Esophagus	oesophagus
4	chr1:173685000-173695200	Weak transcription	Pancreas	Pancrea
5	chr1:173685000-173720800	Weak transcription	Small Intestine	intestine
6	chr1:173685200-173689400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr1:173685200-173690400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr1:173685200-173692200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr1:173685200-173692200	Weak transcription	Placenta	Placenta
10	chr1:173685200-173693400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr1:173685200-173694000	Weak transcription	Left Ventricle	heart
12	chr1:173685200-173694200	Weak transcription	Brain Hippocampus Middle	brain
13	chr1:173685200-173694400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr1:173685200-173694400	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr1:173685200-173694400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr1:173685200-173694400	Weak transcription	Brain Cingulate Gyrus	brain
17	chr1:173685200-173694400	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr1:173685200-173694600	Weak transcription	Colonic Mucosa	Colon
19	chr1:173685200-173724600	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr1:173685400-173690000	Weak transcription	Fetal Muscle Leg	muscle
21	chr1:173685400-173690400	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr1:173685400-173690600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr1:173685400-173690600	Weak transcription	Fetal Muscle Trunk	muscle
24	chr1:173685400-173691200	Weak transcription	Thymus	Thymus
25	chr1:173685400-173691400	Weak transcription	Aorta	Aorta
26	chr1:173685400-173694000	Weak transcription	Primary B cells from peripheral blood	blood
27	chr1:173685400-173694200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr1:173685400-173694400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr1:173685400-173694400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr1:173685400-173694400	Weak transcription	Fetal Brain Male	brain
31	chr1:173685400-173702800	Weak transcription	Psoas Muscle	Psoas
32	chr1:173685400-173725000	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr1:173685600-173691200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr1:173685600-173692200	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr1:173685600-173693800	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr1:173685600-173694200	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr1:173685600-173694600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr1:173685600-173702800	Weak transcription	Brain Substantia Nigra	brain
39	chr1:173685800-173690600	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr1:173685800-173690800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr1:173685800-173692400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr1:173685800-173693600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr1:173685800-173702800	Weak transcription	NH-A	brain
44	chr1:173685800-173703000	Weak transcription	Osteobl	bone
45	chr1:173685800-173724800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr1:173686000-173690600	Weak transcription	Fetal Brain Female	brain
47	chr1:173686000-173693800	Weak transcription	HMEC	breast
48	chr1:173686200-173690600	Weak transcription	Primary B cells from cord blood	blood
49	chr1:173686200-173691200	Weak transcription	Stomach Smooth Muscle	stomach
50	chr1:173686200-173691600	Weak transcription	Primary hematopoietic stem cells	blood

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