Variant report

Variant	rs1327351
Chromosome Location	chr9:108298183-108298184
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	chr9:108295821..108298820-chr9:108299705..108303201,3	MCF-7	breast:
2	chr9:108293123..108295259-chr9:108297045..108298602,2	K562	blood:

Extended variants
information (count: 66 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1018848	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1018849	0.84[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1018850	1.00[YRI][hapmap]
rs1024366	1.00[ASW][hapmap];0.84[CEU][hapmap];0.93[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.81[MEX][hapmap];1.00[YRI][hapmap]
rs10820805	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10820806	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10820807	0.84[CEU][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10820808	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10820816	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10991661	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10991662	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10991664	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10991666	0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10991669	1.00[ASW][hapmap];0.84[CEU][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.81[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10991675	1.00[ASW][hapmap];0.84[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10991680	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10991686	0.87[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs10991688	0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11525961	0.80[AMR][1000 genomes]
rs11535511	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12235779	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12554844	1.00[YRI][hapmap]
rs12555267	0.84[CEU][hapmap];0.93[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1329021	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1329022	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1576285	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16924672	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs16924676	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1858744	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1928293	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][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];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1928294	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2068266	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2518110	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2518111	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2518113	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2518117	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2518118	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2518119	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2518121	1.00[YRI][hapmap]
rs2518122	1.00[ASW][hapmap];0.84[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap];0.81[MEX][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2518127	0.84[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2518132	1.00[ASW][hapmap];0.84[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.81[MEX][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs2518133	1.00[ASW][hapmap];0.93[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.81[AMR][1000 genomes]
rs2768278	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2768282	1.00[ASW][hapmap];0.83[CEU][hapmap];0.93[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.81[MEX][hapmap];1.00[YRI][hapmap]
rs2768284	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2768285	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2768286	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2768287	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2768288	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2768293	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2768295	0.84[CEU][hapmap];0.93[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs2768296	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2904847	1.00[ASW][hapmap];0.84[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.81[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4302902	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56134629	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72744254	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72744266	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72744269	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs885955	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053973	chr9:108199177-108300186	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv615115	chr9:108205262-108298183	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv893692	chr9:108218852-108320988	ZNF genes & repeats Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
4	nsv1050141	chr9:108219667-108317424	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
5	nsv1049133	chr9:108292302-108356068	Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
6	nsv416298	chr9:108295722-108303569	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1327351	OR13D1	cis	cerebellum	SCAN
rs1327351	FKTN	cis	parietal	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108214600-108309800	Weak transcription	HUVEC	blood vessel
2	chr9:108222600-108311400	Weak transcription	Fetal Heart	heart
3	chr9:108242600-108300000	Weak transcription	Brain Anterior Caudate	brain
4	chr9:108268200-108306000	Weak transcription	Brain Angular Gyrus	brain
5	chr9:108272800-108304600	Weak transcription	NHEK	skin
6	chr9:108274400-108299800	Weak transcription	Fetal Lung	lung
7	chr9:108276200-108309200	Weak transcription	Lung	lung
8	chr9:108278800-108305800	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr9:108279000-108311400	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr9:108279000-108317600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr9:108279200-108313000	Weak transcription	Fetal Muscle Trunk	muscle
12	chr9:108282400-108299600	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr9:108282400-108300000	Weak transcription	HSMMtube	muscle
14	chr9:108282400-108302800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr9:108282400-108302800	Weak transcription	HSMM	muscle
16	chr9:108282400-108312400	Weak transcription	HepG2	liver
17	chr9:108282400-108319800	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr9:108282400-108319800	Weak transcription	Left Ventricle	heart
19	chr9:108282400-108319800	Weak transcription	Psoas Muscle	Psoas
20	chr9:108282600-108319800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr9:108289200-108306200	Weak transcription	Fetal Brain Male	brain
22	chr9:108289800-108309800	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr9:108290000-108298800	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr9:108291800-108310200	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr9:108292600-108305600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr9:108292600-108319800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr9:108293600-108299800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr9:108293800-108319800	Weak transcription	Liver	Liver
29	chr9:108294400-108304400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr9:108294600-108299600	Weak transcription	Duodenum Mucosa	Duodenum
31	chr9:108294600-108305200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr9:108294800-108312000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr9:108294800-108319800	Weak transcription	Hela-S3	cervix
34	chr9:108295600-108305800	Weak transcription	Brain Germinal Matrix	brain
35	chr9:108295600-108305800	Weak transcription	Fetal Intestine Large	intestine
36	chr9:108295600-108319800	Weak transcription	Aorta	Aorta
37	chr9:108296200-108302000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr9:108296200-108303000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr9:108296400-108298400	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr9:108296400-108299200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr9:108296400-108316200	Weak transcription	Rectal Smooth Muscle	rectum
42	chr9:108296600-108298800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr9:108296600-108298800	Strong transcription	A549	lung
44	chr9:108296800-108298200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr9:108296800-108298400	Strong transcription	Duodenum Smooth Muscle	Duodenum
46	chr9:108296800-108298800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr9:108296800-108299000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr9:108297000-108298800	Strong transcription	NH-A	brain
49	chr9:108297000-108299000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr9:108297000-108301200	Weak transcription	Osteobl	bone

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