Variant report

Variant	rs1474907
Chromosome Location	chr1:173821022-173821023
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:173793370..173795660-chr1:173820516..173822118,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZBTB37-4	chr1:173820974-173821156	NONHSAT007658

Variant related genes	Relation type
ENSG00000117593	Chromatin interaction
ENSG00000120334	Chromatin interaction

Extended variants
information (count: 100 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10081990	0.93[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10158663	1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10399912	0.86[YRI][hapmap]
rs10798298	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10912677	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10912678	1.00[ASW][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10912680	1.00[ASW][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10912682	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10912684	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1115487	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11487392	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs12067571	0.89[AMR][1000 genomes]
rs12070556	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12073601	0.83[TSI][hapmap]
rs12080389	1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs12082206	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12083423	0.88[AMR][1000 genomes]
rs12085748	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12085894	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12094130	1.00[ASW][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12095090	0.87[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];0.83[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12098124	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs1322771	1.00[ASW][hapmap];0.98[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];1.00[EUR][1000 genomes]
rs1322772	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13375555	0.88[AMR][1000 genomes]
rs16846383	1.00[ASW][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];0.92[YRI][hapmap];0.87[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];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2224657	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28578576	1.00[ASW][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.94[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	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59845733	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6425256	1.00[ASW][hapmap];0.82[YRI][hapmap]
rs6425257	1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6658217	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6663880	1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6675762	1.00[ASW][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6686455	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6689764	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6691327	1.00[ASW][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6691922	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6692452	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]
rs6695782	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6698348	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6702485	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7518130	1.00[ASW][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.83[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7522788	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7534521	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7536773	1.00[ASW][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7544583	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]
rs7550036	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];0.83[AMR][1000 genomes]
rs7552840	1.00[ASW][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9282959	1.00[ASW][hapmap];0.98[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];1.00[EUR][1000 genomes]
rs9282960	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9286886	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9286887	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]
rs9286890	1.00[ASW][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9286894	0.97[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];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9425418	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425419	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425420	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425421	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425422	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425423	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425424	0.96[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	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425431	0.90[MKK][hapmap]
rs9425433	0.84[MKK][hapmap]
rs9425734	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425736	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425738	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425740	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425741	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425742	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9425746	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9425747	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425750	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425751	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425752	1.00[ASW][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425758	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425759	1.00[ASW][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425761	1.00[ASW][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.95[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];0.98[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];1.00[EUR][1000 genomes]
rs9970488	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9970633	1.00[ASW][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
3	esv2757761	chr1:173810642-173955943	Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases
4	esv2758978	chr1:173810642-173955943	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1474907	OR9I1	trans	lymphoblastoid	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173794400-173832800	Weak transcription	Fetal Heart	heart
2	chr1:173794600-173821800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:173794600-173821800	Weak transcription	Pancreas	Pancrea
4	chr1:173794600-173822000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr1:173794600-173832000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr1:173794600-173832000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr1:173794600-173832600	Weak transcription	Brain Substantia Nigra	brain
8	chr1:173794600-173833800	Weak transcription	Stomach Mucosa	stomach
9	chr1:173794800-173834000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr1:173795000-173826200	Weak transcription	Psoas Muscle	Psoas
11	chr1:173795000-173834600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr1:173795200-173822400	Weak transcription	Rectal Smooth Muscle	rectum
13	chr1:173795200-173824600	Weak transcription	Gastric	stomach
14	chr1:173797200-173828400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:173799600-173828800	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr1:173801000-173822200	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr1:173801200-173825000	Weak transcription	Brain Angular Gyrus	brain
18	chr1:173803000-173826600	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr1:173806800-173822800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr1:173809000-173822000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr1:173809200-173825200	Weak transcription	NHDF-Ad	bronchial
22	chr1:173809800-173831800	Weak transcription	Colonic Mucosa	Colon
23	chr1:173810200-173822000	Weak transcription	Fetal Kidney	kidney
24	chr1:173811000-173824600	Weak transcription	Colon Smooth Muscle	Colon
25	chr1:173811000-173825000	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr1:173811200-173822200	Weak transcription	Brain Cingulate Gyrus	brain
27	chr1:173811200-173825000	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr1:173811200-173829200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr1:173811400-173821400	Weak transcription	Osteobl	bone
30	chr1:173813000-173822000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr1:173813200-173821400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr1:173813200-173822000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr1:173813200-173822000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:173813200-173822000	Weak transcription	HSMMtube	muscle
35	chr1:173813200-173823000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr1:173813200-173824800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr1:173813200-173831800	Weak transcription	Right Ventricle	heart
38	chr1:173813200-173832000	Weak transcription	Small Intestine	intestine
39	chr1:173813400-173822000	Weak transcription	Primary B cells from cord blood	blood
40	chr1:173813400-173822000	Weak transcription	NH-A	brain
41	chr1:173813400-173831000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr1:173813600-173821800	Weak transcription	HUVEC	blood vessel
43	chr1:173813600-173822000	Weak transcription	Fetal Lung	lung
44	chr1:173813600-173822200	Weak transcription	Stomach Smooth Muscle	stomach
45	chr1:173813600-173825400	Weak transcription	Brain Anterior Caudate	brain
46	chr1:173814600-173826400	Weak transcription	Hela-S3	cervix
47	chr1:173814800-173822000	Weak transcription	A549	lung
48	chr1:173815000-173826000	Weak transcription	Esophagus	oesophagus
49	chr1:173815200-173821200	Weak transcription	Aorta	Aorta
50	chr1:173815400-173821800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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