Variant report

Variant	rs12665031
Chromosome Location	chr6:45886740-45886741
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10807328	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12204991	0.88[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1361214	0.80[AMR][1000 genomes]
rs1361215	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1416166	0.82[CHD][hapmap]
rs1416167	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.92[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2105168	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3224	0.84[CEU][hapmap]
rs3729618	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777544	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3777546	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3777547	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777548	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777552	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3777553	0.97[AFR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3777554	0.93[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3777556	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3777557	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3777558	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3777559	0.97[AFR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3777561	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.92[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3798258	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3798259	0.97[AFR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3822876	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3822877	0.80[AMR][1000 genomes]
rs3822878	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3822879	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3822880	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3822881	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4714890	0.92[CEU][hapmap];0.80[TSI][hapmap];0.90[EUR][1000 genomes]
rs58427559	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6904888	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.94[TSI][hapmap];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6939554	1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6940409	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9349335	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9349336	0.97[AFR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9367228	0.84[CEU][hapmap];0.81[GIH][hapmap]
rs9367229	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9369590	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9381410	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9381411	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9395134	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9395135	0.94[EUR][1000 genomes];0.88[ASN][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	nsv532024	chr6:45475088-45982640	Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1021917	chr6:45879064-45898314	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
3	esv2757165	chr6:45885642-45887421	Weak transcription Enhancers Strong transcription Genic enhancers	n/a	n/a	inside rSNPs	n/a
4	esv2759424	chr6:45885642-45887421	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12665031	OAT	trans	lymphoblastoid	seeQTL

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45866600-45898400	Weak transcription	Colonic Mucosa	Colon
2	chr6:45868800-45889600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr6:45879800-45889600	Weak transcription	Fetal Muscle Trunk	muscle
4	chr6:45881200-45908000	Weak transcription	Duodenum Mucosa	Duodenum
5	chr6:45882000-45889600	Weak transcription	Adipose Nuclei	Adipose
6	chr6:45882000-45889600	Weak transcription	Lung	lung
7	chr6:45882000-45889600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr6:45882200-45889600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr6:45882200-45890800	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr6:45882200-45891200	Weak transcription	Placenta	Placenta
11	chr6:45882400-45898400	Weak transcription	Fetal Intestine Large	intestine
12	chr6:45883800-45887200	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr6:45884200-45886800	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr6:45884400-45886800	Enhancers	Psoas Muscle	Psoas
15	chr6:45884400-45887200	Genic enhancers	Left Ventricle	heart
16	chr6:45884600-45890400	Weak transcription	Fetal Kidney	kidney
17	chr6:45884800-45887200	Enhancers	Right Ventricle	heart
18	chr6:45884800-45889600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr6:45885200-45889400	Weak transcription	HSMMtube	muscle
20	chr6:45885200-45890400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr6:45885200-45891200	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr6:45885400-45889400	Weak transcription	Fetal Heart	heart
23	chr6:45885800-45889600	Weak transcription	Right Atrium	heart
24	chr6:45886000-45887400	Strong transcription	Fetal Intestine Small	intestine
25	chr6:45886200-45887000	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr6:45886200-45887400	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr6:45886400-45886800	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr6:45886400-45887000	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr6:45886400-45887000	Enhancers	iPS-18 Cell Line	embryonic stem cell
30	chr6:45886400-45887200	Enhancers	H9 Cell Line	embryonic stem cell
31	chr6:45886600-45886800	Enhancers	HUES48 Cell Line	embryonic stem cell
32	chr6:45886600-45887000	Enhancers	iPS-15b Cell Line	embryonic stem cell
33	chr6:45886600-45887200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr6:45886600-45888400	Weak transcription	H1 Cell Line	embryonic stem cell

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