Variant report

Variant	rs6692452
Chromosome Location	chr1:173754505-173754506
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	chr1:173753678..173758387-chr1:173760653..173764131,5	K562	blood:

Variant related genes	Relation type
ENSG00000200674	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];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10158663	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10399912	0.86[YRI][hapmap]
rs10798298	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10912677	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10912678	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][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];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10912682	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10912684	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1115487	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11487392	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs12065033	1.00[TSI][hapmap]
rs12067571	0.89[AMR][1000 genomes]
rs12070556	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12073601	1.00[TSI][hapmap]
rs12080389	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs12082206	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12083423	0.88[AMR][1000 genomes]
rs12085748	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12085894	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][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];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12095090	0.94[AFR][1000 genomes];1.00[AMR][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];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12098124	0.94[AFR][1000 genomes];0.88[AMR][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];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1322772	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13375555	0.85[AFR][1000 genomes];0.88[AMR][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];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16846278	1.00[MEX][hapmap]
rs16846383	1.00[ASW][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];1.00[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];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2224657	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4652283	0.90[MKK][hapmap]
rs4652298	0.90[MKK][hapmap]
rs4652328	0.83[MKK][hapmap]
rs56124923	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59845733	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6425256	1.00[ASW][hapmap];0.82[YRI][hapmap]
rs6425257	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6658217	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6663880	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][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];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6686455	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6689764	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6691922	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6695782	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6698348	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6702485	0.94[AFR][1000 genomes];1.00[AMR][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];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7522788	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7534521	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7544583	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]
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];0.91[AFR][1000 genomes];0.83[AMR][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];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9282960	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9286886	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9286894	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9425418	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425419	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425420	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425421	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425422	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425423	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425424	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425425	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425426	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425431	0.90[MKK][hapmap]
rs9425433	0.85[MKK][hapmap]
rs9425734	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425736	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425738	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425740	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425741	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425742	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9425746	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9425747	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425750	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425751	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425758	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425759	1.00[ASW][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][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];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425768	1.00[ASW][hapmap]
rs9425774	0.83[AMR][1000 genomes]
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];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9970488	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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];0.94[AFR][1000 genomes];1.00[AMR][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	nsv831926	chr1:173702403-173894667	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	291 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6692452	OR9I1	trans	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173726200-173760600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:173728800-173764800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr1:173729800-173781800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:173735800-173781000	Weak transcription	Small Intestine	intestine
5	chr1:173736600-173792400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr1:173736800-173760600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr1:173741400-173757400	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr1:173741800-173759600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr1:173741800-173762400	Weak transcription	Stomach Mucosa	stomach
10	chr1:173742800-173759800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr1:173743200-173755400	Strong transcription	Primary B cells from peripheral blood	blood
12	chr1:173743200-173757200	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr1:173743200-173758800	Strong transcription	Primary T cells from cord blood	blood
14	chr1:173743400-173755600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:173743400-173757200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:173743400-173757200	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr1:173743400-173757400	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr1:173743400-173757800	Strong transcription	Dnd41	blood
19	chr1:173743400-173758000	Strong transcription	Fetal Thymus	thymus
20	chr1:173743600-173755400	Strong transcription	Adipose Nuclei	Adipose
21	chr1:173744800-173790200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr1:173745000-173767400	Weak transcription	NHEK	skin
23	chr1:173745000-173792400	Weak transcription	Psoas Muscle	Psoas
24	chr1:173745200-173765200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr1:173745800-173759600	Strong transcription	Liver	Liver
26	chr1:173746200-173754600	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr1:173746800-173757200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr1:173746800-173757200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr1:173746800-173757200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr1:173747200-173757200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr1:173747400-173755400	Strong transcription	Duodenum Mucosa	Duodenum
32	chr1:173747400-173756600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr1:173747400-173757200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr1:173747800-173769200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr1:173748600-173755400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr1:173748600-173757200	Strong transcription	Placenta	Placenta
37	chr1:173748600-173757400	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr1:173748600-173759000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr1:173748800-173755000	Strong transcription	Left Ventricle	heart
40	chr1:173748800-173755400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr1:173748800-173755400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr1:173748800-173757600	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr1:173748800-173757600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr1:173749000-173754600	Strong transcription	Fetal Muscle Leg	muscle
45	chr1:173749000-173754800	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr1:173749000-173755200	Strong transcription	Primary hematopoietic stem cells	blood
47	chr1:173749000-173755200	Strong transcription	Fetal Intestine Large	intestine
48	chr1:173749000-173755400	Strong transcription	Sigmoid Colon	Sigmoid Colon
49	chr1:173749000-173755400	Strong transcription	GM12878-XiMat	blood
50	chr1:173749000-173757200	Strong transcription	Rectal Mucosa Donor 31	rectum

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