Variant report

Variant	rs9389034
Chromosome Location	chr6:133138010-133138011
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:111)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:111 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:133133973-133142719	H1-hESC	embryonic stem cell:	n/a	n/a
2	CTCF	chr6:133137860-133138010	GM12872	blood:	n/a	n/a
3	CTCF	chr6:133137860-133138010	HA-sp	spinal cord:	n/a	n/a
4	CTCF	chr6:133137880-133138030	GM12864	blood:	n/a	n/a
5	POLR2A	chr6:133136894-133138284	PANC-1	pancreas:	n/a	n/a
6	POLR2A	chr6:133134162-133138350	GM12892	blood:	n/a	n/a
7	POLR2A	chr6:133133509-133142958	HepG2	liver:	n/a	n/a
8	MYC	chr6:133133521-133138056	K562	blood:	n/a	chr6:133134081-133134091 chr6:133135767-133135777
9	CTCF	chr6:133137860-133138010	GM12865	blood:	n/a	n/a
10	POLR2A	chr6:133134007-133138262	GM15510	blood:	n/a	n/a
11	CTCF	chr6:133137860-133138010	HepG2	liver:	n/a	n/a
12	POLR2A	chr6:133134121-133142902	PFSK-1	brain:	n/a	n/a
13	POLR2A	chr6:133135219-133144621	HepG2	liver:	n/a	n/a
14	POLR2A	chr6:133135075-133142824	K562	blood:	n/a	n/a
15	CTCF	chr6:133137900-133138050	HPAF	blood vessel:	n/a	n/a
16	POLR2A	chr6:133134120-133142624	GM18505	blood:	n/a	n/a
17	CTCF	chr6:133137940-133138090	BE2_C	brain:	n/a	n/a
18	CTCF	chr6:133137860-133138010	NHEK	skin:	n/a	n/a
19	CTCF	chr6:133137925-133138013	GM19239	blood:	n/a	n/a
20	TAF7	chr6:133134418-133138128	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr6:133133442-133144695	MCF10A-Er-Src	breast:	n/a	n/a
22	CTCF	chr6:133137920-133138070	GM06990	blood:	n/a	n/a
23	CTCF	chr6:133137880-133138030	GM12871	blood:	n/a	n/a
24	POLR2A	chr6:133133522-133142994	GM12891	blood:	n/a	n/a
25	CTCF	chr6:133137900-133138050	MCF-7	breast:	n/a	n/a
26	CTCF	chr6:133137860-133138010	HCPEpiC	choroid plexus:	n/a	n/a
27	CHD2	chr6:133137694-133142877	H1-hESC	embryonic stem cell:	n/a	n/a
28	SMC3	chr6:133137886-133138154	GM12878	blood:	n/a	n/a
29	POLR2A	chr6:133135035-133138163	U87	brain:	n/a	n/a
30	CTCF	chr6:133137924-133138028	GM12878	blood:	n/a	n/a
31	POLR2A	chr6:133137328-133142813	GM12878	blood:	n/a	n/a
32	POLR2A	chr6:133133648-133142538	K562	blood:	n/a	n/a
33	POLR2A	chr6:133137026-133138035	K562	blood:	n/a	n/a
34	POLR2A	chr6:133136985-133138228	GM12891	blood:	n/a	n/a
35	CTCF	chr6:133137920-133138070	BJ	skin:	n/a	n/a
36	CTCF	chr6:133137914-133138036	MCF-7	breast:	n/a	n/a
37	MXI1	chr6:133137566-133138034	GM12878	blood:	n/a	n/a
38	POLR2A	chr6:133134946-133142915	U87	brain:	n/a	n/a
39	CTCF	chr6:133137926-133138018	GM13976	blood:	n/a	n/a
40	POLR2A	chr6:133134298-133142858	Hela-S3	cervix:	n/a	n/a
41	POLR2A	chr6:133133488-133142945	PBDE	blood:	n/a	n/a
42	CTCF	chr6:133138009-133138018	LNCaP	prostate:	n/a	n/a
43	POLR2A	chr6:133133410-133142612	HepG2	liver:	n/a	n/a
44	POLR2A	chr6:133133546-133143142	SK-N-MC	brain:	n/a	n/a
45	SP1	chr6:133137972-133138381	H1-hESC	embryonic stem cell:	n/a	n/a
46	POLR2A	chr6:133137037-133138286	GM12891	blood:	n/a	n/a
47	CTCF	chr6:133137921-133138020	Hela-S3	cervix:	n/a	n/a
48	POLR2A	chr6:133136910-133143141	MCF-7	breast:	n/a	n/a
49	POLR2A	chr6:133137198-133138298	SK-N-SH	brain:	n/a	n/a
50	POLR2A	chr6:133133528-133143521	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:133054032..133057251-chr6:133136548..133139421,3	K562	blood:
2	chr17:40214097..40215598-chr6:133136759..133139699,2	K562	blood:
3	chr6:133049609..133052376-chr6:133137041..133138744,2	MCF-7	breast:
4	chr6:132855902..132859597-chr6:133135974..133139810,3	K562	blood:
5	chr6:133118544..133124606-chr6:133132137..133138834,13	MCF-7	breast:
6	chr6:133117688..133126502-chr6:133133829..133139054,19	MCF-7	breast:

No data

Variant related genes	Relation type
SNORA33	TF binding region
ENSG00000093134	Chromatin interaction
ENSG00000237110	Chromatin interaction
ENSG00000187595	Chromatin interaction
ENSG00000146409	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10457594	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11154696	0.91[MEX][hapmap]
rs1124450	0.86[CHD][hapmap]
rs12200907	0.89[CHD][hapmap]
rs12202302	0.85[CHB][hapmap];0.83[CHD][hapmap];0.87[MEX][hapmap]
rs12206120	0.81[ASN][1000 genomes]
rs1359142	0.89[CHD][hapmap]
rs1408062	0.89[CHD][hapmap]
rs2236381	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2236382	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];1.00[YRI][hapmap]
rs35893416	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756968	0.90[ASN][1000 genomes]
rs4599669	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4897617	0.88[CHD][hapmap]
rs6569853	0.82[ASN][1000 genomes]
rs6569854	0.82[ASN][1000 genomes]
rs6920271	0.89[ASN][1000 genomes]
rs6926466	0.85[CHB][hapmap];0.83[CHD][hapmap];0.87[MEX][hapmap]
rs7452703	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs755895	0.81[ASN][1000 genomes]
rs761125	0.85[CHB][hapmap]
rs7751879	0.86[CEU][hapmap];0.85[CHB][hapmap]
rs7756588	0.89[CHD][hapmap]
rs7764152	0.85[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs9321374	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9373030	0.89[CHD][hapmap]
rs9399043	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9399044	0.95[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9402457	0.89[ASN][1000 genomes]
rs9493450	0.83[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs9493451	0.89[CHB][hapmap]
rs9493458	0.86[CEU][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];0.83[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv970167	chr6:133137525-133138525	Strong transcription Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Active TSS Enhancers	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9389034	SNORA33	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:133134000-133138400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:133134600-133138400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
3	chr6:133135800-133138400	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
4	chr6:133136000-133138200	Transcr. at gene 5' and 3'	Dnd41	blood
5	chr6:133136000-133138200	Transcr. at gene 5' and 3'	NHEK	skin
6	chr6:133136000-133138200	Transcr. at gene 5' and 3'	Osteobl	bone
7	chr6:133136000-133138400	Transcr. at gene 5' and 3'	iPS-15b Cell Line	embryonic stem cell
8	chr6:133136000-133138400	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
9	chr6:133136000-133138400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr6:133136000-133138400	Transcr. at gene 5' and 3'	HMEC	breast
11	chr6:133136000-133138600	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
12	chr6:133136000-133139000	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
13	chr6:133136000-133139200	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
14	chr6:133136000-133139200	Transcr. at gene 5' and 3'	K562	blood
15	chr6:133136000-133139800	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr6:133136200-133138200	Transcr. at gene 5' and 3'	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr6:133136200-133138200	Transcr. at gene 5' and 3'	Hela-S3	cervix
18	chr6:133136200-133138400	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr6:133136200-133138400	Transcr. at gene 5' and 3'	NHLF	lung
20	chr6:133136200-133138600	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr6:133136200-133138600	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr6:133136200-133138600	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
23	chr6:133136200-133139000	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr6:133136200-133139000	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
25	chr6:133136200-133139400	Transcr. at gene 5' and 3'	A549	lung
26	chr6:133136200-133140600	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
27	chr6:133136400-133138200	Transcr. at gene 5' and 3'	NH-A	brain
28	chr6:133136400-133138400	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr6:133136400-133138400	Transcr. at gene 5' and 3'	HUVEC	blood vessel
30	chr6:133136600-133138400	Transcr. at gene 5' and 3'	HepG2	liver
31	chr6:133136600-133139000	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr6:133136800-133138600	Transcr. at gene 5' and 3'	Fetal Kidney	kidney
33	chr6:133137000-133138200	Transcr. at gene 5' and 3'	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr6:133137000-133138200	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr6:133137000-133139200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr6:133137200-133138200	Transcr. at gene 5' and 3'	ES-UCSF4 Cell Line	embryonic stem cell
37	chr6:133137200-133138200	Transcr. at gene 5' and 3'	Duodenum Smooth Muscle	Duodenum
38	chr6:133137200-133145400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr6:133137400-133138400	Genic enhancers	Primary B cells from cord blood	blood
40	chr6:133137400-133138800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr6:133137400-133139600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr6:133137400-133141000	Strong transcription	Primary neutrophils fromperipheralblood	blood
43	chr6:133137400-133141000	Strong transcription	Aorta	Aorta
44	chr6:133137400-133141200	Genic enhancers	Skeletal Muscle Female	skeletal muscle
45	chr6:133137400-133141400	Strong transcription	Fetal Muscle Trunk	muscle
46	chr6:133137600-133138200	Genic enhancers	Brain Germinal Matrix	brain
47	chr6:133137600-133138200	Genic enhancers	Colonic Mucosa	Colon
48	chr6:133137600-133138400	Enhancers	Stomach Mucosa	stomach
49	chr6:133137600-133138600	Genic enhancers	Fetal Brain Female	brain
50	chr6:133137600-133138800	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood

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