Variant report

Variant	rs6926466
Chromosome Location	chr6:133135413-133135414
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:534)
CpG islands
(count:0)
Chromatin interactive
region (count:26)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:534 , 50 per page) page: 1 2 3 4 5 6 7 ... 11

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TBL1XR1	chr6:133135143-133136914	K562	blood:	n/a	n/a
2	TCF12	chr6:133134391-133136145	A549	lung:	n/a	n/a
3	POLR2A	chr6:133135039-133136794	GM12878	blood:	n/a	n/a
4	POLR2A	chr6:133133973-133142719	H1-hESC	embryonic stem cell:	n/a	n/a
5	FOS	chr6:133135356-133135668	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr6:133134002-133136170	HCT-116	colon:	n/a	n/a
7	POLR2A	chr6:133135088-133136727	SK-N-SH	brain:	n/a	n/a
8	FOXA1	chr6:133135063-133135825	HepG2	liver:	n/a	n/a
9	USF1	chr6:133135245-133135516	A549	lung:	n/a	n/a
10	WRNIP1	chr6:133135124-133136519	GM12878	blood:	n/a	n/a
11	NFIC	chr6:133135035-133136093	HepG2	liver:	n/a	n/a
12	SIN3AK20	chr6:133135113-133135946	PFSK-1	brain:	n/a	n/a
13	CTCF	chr6:133135303-133135774	GM12878	blood:	n/a	n/a
14	EP300	chr6:133135173-133135915	A549	lung:	n/a	n/a
15	POLR2A	chr6:133135032-133137592	HCT-116	colon:	n/a	n/a
16	TEAD4	chr6:133135032-133136666	K562	blood:	n/a	n/a
17	NR2F2	chr6:133134573-133136044	K562	blood:	n/a	n/a
18	TAF1	chr6:133134632-133136152	H1-hESC	embryonic stem cell:	n/a	n/a
19	KAT2A	chr6:133135346-133135883	GM12878	blood:	n/a	n/a
20	NRF1	chr6:133135186-133135887	GM12878	blood:	n/a	chr6:133135648-133135662 chr6:133135647-133135658 chr6:133135650-133135659 chr6:133135648-133135659
21	EP300	chr6:133135135-133135833	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr6:133134162-133138350	GM12892	blood:	n/a	n/a
23	POLR2A	chr6:133135005-133136562	HepG2	liver:	n/a	n/a
24	TCF7L2	chr6:133135295-133135765	PANC-1	pancreas:	n/a	n/a
25	POLR2A	chr6:133133509-133142958	HepG2	liver:	n/a	n/a
26	CREB1	chr6:133135148-133135926	A549	lung:	n/a	n/a
27	ETS1	chr6:133135219-133135859	K562	blood:	n/a	n/a
28	POLR2A	chr6:133134992-133136843	K562	blood:	n/a	n/a
29	SMC3	chr6:133135208-133135934	K562	blood:	n/a	n/a
30	STAT5A	chr6:133134219-133136486	GM12878	blood:	n/a	chr6:133134283-133134294 chr6:133134277-133134288 chr6:133135591-133135602 chr6:133134635-133134644 chr6:133134636-133134645
31	SIN3AK20	chr6:133135164-133135943	A549	lung:	n/a	n/a
32	POLR2A	chr6:133135043-133136381	GM12878	blood:	n/a	n/a
33	TAF1	chr6:133135053-133136053	MCF-7	breast:	n/a	n/a
34	POLR2A	chr6:133134236-133136890	MCF-7	breast:	n/a	n/a
35	ZNF143	chr6:133135168-133135864	H1-hESC	embryonic stem cell:	n/a	n/a
36	RFX5	chr6:133135164-133135990	HepG2	liver:	n/a	n/a
37	MXI1	chr6:133135103-133136685	IMR90	lung:	n/a	n/a
38	TBP	chr6:133133860-133135952	Hela-S3	cervix:	n/a	n/a
39	CEBPD	chr6:133135193-133135999	HepG2	liver:	n/a	n/a
40	POLR2A	chr6:133135037-133136507	GM12891	blood:	n/a	n/a
41	PML	chr6:133135217-133136112	GM12878	blood:	n/a	n/a
42	MYC	chr6:133133521-133138056	K562	blood:	n/a	chr6:133134081-133134091 chr6:133135767-133135777
43	THAP1	chr6:133135279-133135802	K562	blood:	n/a	n/a
44	MTA3	chr6:133135037-133135967	GM12878	blood:	n/a	n/a
45	NR3C1	chr6:133135175-133135703	A549	lung:	n/a	n/a
46	POLR2A	chr6:133134007-133138262	GM15510	blood:	n/a	n/a
47	REST	chr6:133135059-133135974	PFSK-1	brain:	n/a	n/a
48	TEAD4	chr6:133135241-133135933	A549	lung:	n/a	n/a
49	BCLAF1	chr6:133135173-133136084	K562	blood:	n/a	n/a
50	TEAD4	chr6:133135254-133135912	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:26 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:77656072..77656696-chr6:133135247..133136163,2	Hela-S3	cervix:
2	chr6:133084942..133087324-chr6:133134860..133137280,2	MCF-7	breast:
3	chr6:133135254..133135853-chr7:99698047..99698863,2	NB4	blood:
4	chr6:133133722..133135487-chr6:133500551..133504315,3	K562	blood:
5	chr14:69259781..69261291-chr6:133134489..133136848,2	MCF-7	breast:
6	chr1:150039196..150039749-chr6:133135355..133136176,2	Hela-S3	cervix:
7	chr6:133132887..133135811-chr6:134273188..134277510,5	K562	blood:
8	chr12:46121390..46121921-chr6:133134920..133135826,2	Hela-S3	cervix:
9	chr6:133135395..133135910-chr9:102668805..102669502,2	MCF-7	breast:
10	chr5:171614819..171615648-chr6:133135259..133136064,2	Hela-S3	cervix:
11	chr15:63449130..63449939-chr6:133135315..133135869,2	Hela-S3	cervix:
12	chr6:133135261..133136170-chr7:7680235..7681119,2	Hela-S3	cervix:
13	chr6:132832429..132834669-chr6:133134284..133137002,3	K562	blood:
14	chr6:132965299..132967214-chr6:133134332..133136020,2	K562	blood:
15	chr17:79479507..79480059-chr6:133135411..133136304,2	HCT-116	colon:
16	chr19:58873348..58874285-chr6:133135194..133136031,2	Hela-S3	cervix:
17	chr6:133135224..133137195-chr7:86974442..86977103,2	MCF-7	breast:
18	chr1:853806..855355-chr6:133134480..133137289,2	MCF-7	breast:
19	chr6:133084415..133087080-chr6:133134762..133137402,2	MCF-7	breast:
20	chr6:133118544..133124606-chr6:133132137..133138834,13	MCF-7	breast:
21	chr6:133134320..133137127-chr6:136569335..136571574,2	K562	blood:
22	chr6:132833194..132835178-chr6:133134140..133136704,2	MCF-7	breast:
23	chr6:132994919..132997703-chr6:133134162..133135954,3	MCF-7	breast:
24	chr6:133117688..133126502-chr6:133133829..133139054,19	MCF-7	breast:
25	chr1:159894871..159895411-chr6:133135389..133136277,2	Hela-S3	cervix:
26	chr1:33429448..33430407-chr6:133134991..133135963,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
SNORD101	TF binding region
SNORD100	TF binding region
SNORA33	TF binding region
RPS12	TF binding region
ENSG00000185650	Chromatin interaction
ENSG00000106399	Chromatin interaction
ENSG00000166508	Chromatin interaction
ENSG00000268230	Chromatin interaction
ENSG00000136874	Chromatin interaction
ENSG00000174586	Chromatin interaction
ENSG00000269054	Chromatin interaction
ENSG00000079950	Chromatin interaction
ENSG00000146409	Chromatin interaction
ENSG00000218194	Chromatin interaction
ENSG00000219545	Chromatin interaction
ENSG00000185088	Chromatin interaction
ENSG00000146410	Chromatin interaction
ENSG00000112303	Chromatin interaction
ENSG00000184009	Chromatin interaction
ENSG00000158710	Chromatin interaction
ENSG00000136631	Chromatin interaction
ENSG00000223764	Chromatin interaction
ENSG00000072786	Chromatin interaction
ENSG00000255145	Chromatin interaction
ENSG00000005469	Chromatin interaction
ENSG00000271488	Chromatin interaction
ENSG00000085365	Chromatin interaction
ENSG00000146399	Chromatin interaction
ENSG00000273015	Chromatin interaction
ENSG00000116514	Chromatin interaction
ENSG00000182165	Chromatin interaction
ENSG00000028839	Chromatin interaction
ENSG00000245556	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1009687	0.80[JPT][hapmap]
rs11154696	0.89[CEU][hapmap];0.89[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12202302	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1408065	0.80[JPT][hapmap]
rs1983607	0.93[CEU][hapmap];0.87[CHB][hapmap];0.83[JPT][hapmap];0.88[EUR][1000 genomes]
rs2236381	0.85[CHB][hapmap];0.83[CHD][hapmap];0.88[MEX][hapmap]
rs2236382	0.85[CHB][hapmap];0.83[CHD][hapmap];0.88[MEX][hapmap]
rs271179	0.80[JPT][hapmap]
rs3756969	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3778174	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4599669	0.85[CHB][hapmap];0.88[MEX][hapmap]
rs6569855	0.84[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs6907421	0.91[CHD][hapmap]
rs6921262	0.88[ASN][1000 genomes]
rs6927761	0.88[CEU][hapmap];0.84[CHB][hapmap];0.87[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs761125	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7740291	0.80[JPT][hapmap]
rs7768053	0.91[CHD][hapmap];0.81[TSI][hapmap]
rs7774585	0.91[CHD][hapmap]
rs9321374	0.85[CHB][hapmap];0.88[MEX][hapmap]
rs9321378	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9373033	0.80[JPT][hapmap]
rs9375921	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9375927	0.94[CHD][hapmap];0.86[GIH][hapmap];0.80[JPT][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap]
rs9385624	0.80[JPT][hapmap]
rs9389034	0.85[CHB][hapmap];0.83[CHD][hapmap];0.87[MEX][hapmap]
rs9389035	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9399043	0.85[CHB][hapmap]
rs9402461	0.91[CHD][hapmap]
rs9493450	0.81[CHB][hapmap]
rs9493451	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9493458	0.83[CHD][hapmap]
rs9493459	0.89[CEU][hapmap];0.97[CHD][hapmap];0.80[GIH][hapmap];0.80[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[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	nsv532069	chr6:132776411-133462292	Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv1015742	chr6:132933666-133285852	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
3	nsv886676	chr6:133111706-133168582	Flanking Active TSS Genic enhancers Enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
4	esv1806734	chr6:133125643-133168582	Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6926466	TMEM200A	cis	cerebellum	SCAN
rs6926466	ACA33	cis	multi-tissue	Pritchard
rs6926466	SNORA33	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:133133400-133135800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr6:133133400-133136000	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr6:133133400-133136000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr6:133133400-133136200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr6:133133400-133136200	Active TSS	NHDF-Ad	bronchial
6	chr6:133133400-133136400	Active TSS	Rectal Mucosa Donor 29	rectum
7	chr6:133133600-133136000	Active TSS	H1 Cell Line	embryonic stem cell
8	chr6:133133600-133136000	Active TSS	H9 Cell Line	embryonic stem cell
9	chr6:133133600-133136000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr6:133133600-133136000	Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr6:133133600-133136000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
12	chr6:133133600-133136000	Active TSS	Fetal Lung	lung
13	chr6:133133600-133136200	Active TSS	Brain Substantia Nigra	brain
14	chr6:133133600-133136400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
15	chr6:133133600-133136400	Active TSS	Brain Angular Gyrus	brain
16	chr6:133133600-133136400	Active TSS	Brain Anterior Caudate	brain
17	chr6:133133600-133136600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr6:133133600-133136600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
19	chr6:133133600-133136800	Active TSS	Brain Cingulate Gyrus	brain
20	chr6:133133600-133137000	Active TSS	Aorta	Aorta
21	chr6:133133600-133137000	Active TSS	Fetal Intestine Small	intestine
22	chr6:133133600-133137000	Active TSS	Ovary	ovary
23	chr6:133133600-133137000	Active TSS	Thymus	Thymus
24	chr6:133133600-133137200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
25	chr6:133133600-133137200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
26	chr6:133133600-133137200	Active TSS	Colonic Mucosa	Colon
27	chr6:133133800-133135800	Active TSS	HUES6 Cell Line	embryonic stem cell
28	chr6:133133800-133136000	Active TSS	Rectal Mucosa Donor 31	rectum
29	chr6:133133800-133136200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr6:133133800-133136200	Active TSS	Stomach Smooth Muscle	stomach
31	chr6:133133800-133136400	Active TSS	Fetal Thymus	thymus
32	chr6:133133800-133136600	Active TSS	Colon Smooth Muscle	Colon
33	chr6:133133800-133136600	Active TSS	Small Intestine	intestine
34	chr6:133133800-133136800	Active TSS	Fetal Muscle Trunk	muscle
35	chr6:133133800-133136800	Active TSS	Placenta	Placenta
36	chr6:133133800-133136800	Active TSS	Fetal Stomach	stomach
37	chr6:133133800-133137000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr6:133133800-133137000	Active TSS	Fetal Intestine Large	intestine
39	chr6:133133800-133137000	Active TSS	Right Ventricle	heart
40	chr6:133133800-133137000	Active TSS	Sigmoid Colon	Sigmoid Colon
41	chr6:133133800-133137000	Active TSS	Stomach Mucosa	stomach
42	chr6:133133800-133137200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr6:133134000-133136000	Active TSS	HUES48 Cell Line	embryonic stem cell
44	chr6:133134000-133136000	Active TSS	HUES64 Cell Line	embryonic stem cell
45	chr6:133134000-133136000	Active TSS	iPS-18 Cell Line	embryonic stem cell
46	chr6:133134000-133136000	Active TSS	Brain Inferior Temporal Lobe	brain
47	chr6:133134000-133136000	Active TSS	HMEC	breast
48	chr6:133134000-133136000	Active TSS	K562	blood
49	chr6:133134000-133136200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr6:133134000-133136200	Active TSS	Breast Myoepithelial Primary Cells	Breast

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