Variant report

Variant	rs3777554
Chromosome Location	chr6:45888980-45888981
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RELA	chr6:45888552-45889172	GM12878	blood:	n/a	n/a
2	MEF2C	chr6:45888473-45889062	GM12878	blood:	n/a	n/a
3	WRNIP1	chr6:45888517-45889026	GM12878	blood:	n/a	n/a
4	FOXM1	chr6:45888447-45889180	GM12878	blood:	n/a	chr6:45888460-45888468
5	NFATC1	chr6:45888489-45889035	GM12878	blood:	n/a	n/a
6	MXI1	chr6:45888740-45889193	GM12878	blood:	n/a	n/a
7	IRF4	chr6:45888424-45889075	GM12878	blood:	n/a	n/a
8	EP300	chr6:45888470-45889205	GM12878	blood:	n/a	chr6:45888728-45888737
9	BCL11A	chr6:45888416-45889028	GM12878	blood:	n/a	chr6:45888729-45888738 chr6:45888728-45888737
10	BCL3	chr6:45888520-45888982	GM12878	blood:	n/a	chr6:45888729-45888738 chr6:45888728-45888737
11	TBP	chr6:45888594-45889032	GM12878	blood:	n/a	n/a
12	BCLAF1	chr6:45888478-45889034	GM12878	blood:	n/a	chr6:45888729-45888738 chr6:45888728-45888737
13	EP300	chr6:45888495-45889163	GM12878	blood:	n/a	chr6:45888728-45888737
14	NFIC	chr6:45888381-45889120	GM12878	blood:	n/a	n/a
15	RELA	chr6:45888575-45889040	GM10847	blood:	n/a	n/a
16	TCF12	chr6:45888590-45889008	GM12878	blood:	n/a	n/a
17	RCOR1	chr6:45888487-45888989	GM12878	blood:	n/a	n/a
18	RUNX3	chr6:45888471-45889236	GM12878	blood:	n/a	n/a
19	SREBP1	chr6:45887976-45889155	GM12878	blood:	n/a	n/a
20	MTA3	chr6:45888534-45889062	GM12878	blood:	n/a	n/a
21	BCLAF1	chr6:45888586-45889159	GM12878	blood:	n/a	chr6:45888729-45888738 chr6:45888728-45888737
22	NFIC	chr6:45888281-45889364	GM12878	blood:	n/a	n/a
23	YY1	chr6:45888750-45889194	GM12878	blood:	n/a	n/a
24	STAT5A	chr6:45888503-45889085	GM12878	blood:	n/a	chr6:45888729-45888738 chr6:45888728-45888737
25	MEF2A	chr6:45888478-45889088	GM12878	blood:	n/a	n/a
26	SP1	chr6:45888582-45888980	GM12878	blood:	n/a	chr6:45888670-45888679 chr6:45888669-45888683
27	CEBPB	chr6:45888428-45889111	GM12878	blood:	n/a	chr6:45888753-45888764
28	NFATC1	chr6:45888496-45889142	GM12878	blood:	n/a	n/a
29	RELA	chr6:45888604-45889171	GM18505	blood:	n/a	n/a
30	BATF	chr6:45888464-45889068	GM12878	blood:	n/a	chr6:45888726-45888736 chr6:45888725-45888736
31	PAX5	chr6:45888455-45889179	GM12878	blood:	n/a	n/a
32	ZNF143	chr6:45888634-45889058	GM12878	blood:	n/a	n/a
33	TBL1XR1	chr6:45888558-45889140	GM12878	blood:	n/a	n/a
34	MEF2A	chr6:45888524-45889025	GM12878	blood:	n/a	n/a
35	PML	chr6:45888544-45889127	GM12878	blood:	n/a	n/a
36	CHD2	chr6:45888431-45889128	GM12878	blood:	n/a	n/a
37	CUX1	chr6:45888861-45889137	GM12878	blood:	n/a	n/a
38	IKZF1	chr6:45888465-45889129	GM12878	blood:	n/a	n/a
39	MAZ	chr6:45888504-45889065	GM12878	blood:	n/a	chr6:45888728-45888737 chr6:45888729-45888738
40	POLR2A	chr6:45888507-45889068	GM12892	blood:	n/a	n/a
41	STAT3	chr6:45888637-45889005	GM12878	blood:	n/a	chr6:45888729-45888738 chr6:45888728-45888737
42	EBF1	chr6:45888483-45889253	GM12878	blood:	n/a	n/a
43	POU2F2	chr6:45888399-45889045	GM12878	blood:	n/a	n/a
44	MTA3	chr6:45888402-45889219	GM12878	blood:	n/a	n/a
45	RUNX3	chr6:45888446-45889160	GM12878	blood:	n/a	n/a
46	ATF2	chr6:45888487-45889088	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
CLIC5	TF binding region

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10807328	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12204991	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12665031	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]
rs1361215	0.93[AFR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1416166	0.84[CHD][hapmap];0.83[JPT][hapmap];0.88[MEX][hapmap];0.84[AMR][1000 genomes]
rs1416167	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2105168	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2894657	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3729618	0.93[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.87[LWK][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3777544	0.80[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs3777546	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3777547	0.92[AFR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3777548	0.93[AFR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3777552	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3777553	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3777556	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3777557	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3777558	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3777559	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3777561	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3798258	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3798259	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3822876	0.89[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3822878	0.93[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3822879	0.93[AFR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3822880	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3822881	0.89[AFR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4714890	1.00[CEU][hapmap];0.82[TSI][hapmap];0.91[EUR][1000 genomes]
rs58427559	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6904888	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6939554	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6940409	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9349335	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9349336	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9367228	0.81[GIH][hapmap]
rs9367229	0.93[AFR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9369590	0.93[AFR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9381410	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9381411	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9395134	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9395135	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3777554	OAT	trans	lymphoblastoid	seeQTL

Chromatin state (count:40 , 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	chr6:45884600-45890400	Weak transcription	Fetal Kidney	kidney
13	chr6:45884800-45889600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr6:45885200-45889400	Weak transcription	HSMMtube	muscle
15	chr6:45885200-45890400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr6:45885200-45891200	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr6:45885400-45889400	Weak transcription	Fetal Heart	heart
18	chr6:45885800-45889600	Weak transcription	Right Atrium	heart
19	chr6:45886800-45889600	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr6:45886800-45892000	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr6:45886800-45910600	Weak transcription	Psoas Muscle	Psoas
22	chr6:45887000-45890400	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr6:45887000-45892000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr6:45887200-45889000	Weak transcription	Right Ventricle	heart
25	chr6:45887200-45889400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr6:45887200-45889400	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr6:45887400-45896600	Weak transcription	Fetal Intestine Small	intestine
28	chr6:45887800-45892800	Enhancers	GM12878-XiMat	blood
29	chr6:45888400-45889000	Enhancers	NH-A	brain
30	chr6:45888400-45889200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr6:45888400-45889600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr6:45888400-45889600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr6:45888400-45890000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr6:45888400-45890000	Genic enhancers	Left Ventricle	heart
35	chr6:45888400-45890200	Enhancers	Fetal Muscle Leg	muscle
36	chr6:45888400-45892200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr6:45888400-45892800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr6:45888600-45890400	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr6:45888600-45892400	Enhancers	HSMM	muscle
40	chr6:45888800-45889000	Enhancers	Osteobl	bone

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