Variant report

Variant	rs9503909
Chromosome Location	chr6:4059542-4059543
allele	C/G
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	POLR2A	chr6:4059483-4059624	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr6:4059306-4059759	SK-N-SH	brain:	n/a	n/a
3	FOSL1	chr6:4059345-4059661	K562	blood:	n/a	n/a
4	MYC	chr6:4059284-4059744	MCF10A-Er-Src	breast:	n/a	n/a
5	CTCF	chr6:4059500-4059650	K562	blood:	n/a	n/a
6	CTCF	chr6:4059440-4059590	A549	lung:	n/a	n/a
7	FOS	chr6:4059333-4059785	MCF10A-Er-Src	breast:	n/a	chr6:4059572-4059583 chr6:4059690-4059699
8	POLR2A	chr6:4059419-4059610	Hela-S3	cervix:	n/a	n/a
9	CTCF	chr6:4059440-4059590	HEEpiC	esophagus:	n/a	n/a
10	JUND	chr6:4059219-4059941	SK-N-SH	brain:	n/a	chr6:4059690-4059699
11	CTCF	chr6:4059420-4059570	HUVEC	blood vessel:	n/a	n/a
12	FOSL2	chr6:4059246-4059833	A549	lung:	n/a	chr6:4059690-4059699
13	EP300	chr6:4059273-4059939	SK-N-SH	brain:	n/a	chr6:4059816-4059826
14	CTCF	chr6:4059440-4059590	Hela-S3	cervix:	n/a	n/a
15	CTCF	chr6:4059440-4059590	HPF	lung:	n/a	n/a
16	CTCF	chr6:4059490-4059566	K562	blood:	n/a	n/a
17	JUN	chr6:4059234-4060480	K562	blood:	n/a	chr6:4059690-4059699
18	RXRA	chr6:4059270-4059896	SK-N-SH	brain:	n/a	n/a
19	CTCF	chr6:4059440-4059590	AG09309	skin:	n/a	n/a
20	FOSL2	chr6:4059411-4059772	SK-N-SH	brain:	n/a	chr6:4059690-4059699
21	CTCF	chr6:4059460-4059610	AG04449	skin:	n/a	n/a
22	JUN	chr6:4059452-4059714	HepG2	liver:	n/a	chr6:4059690-4059699
23	RAD21	chr6:4059349-4059695	SK-N-SH_RA	brain:	n/a	n/a
24	GABPA	chr6:4059487-4059719	A549	lung:	n/a	n/a
25	CTCF	chr6:4059440-4059590	HCFaa	heart:	n/a	n/a
26	CTCF	chr6:4059400-4059550	HBMEC	blood vessel:	n/a	n/a
27	CTCF	chr6:4059460-4059610	BJ	skin:	n/a	n/a
28	HNF4G	chr6:4059405-4059748	HepG2	liver:	n/a	chr6:4059539-4059551 chr6:4059538-4059553
29	HDAC2	chr6:4059307-4059664	HepG2	liver:	n/a	n/a
30	CTCF	chr6:4059496-4059580	Fibrobl	skin:	n/a	n/a
31	CTCF	chr6:4059440-4059590	RPTEC	kidney:	n/a	n/a
32	FOSL2	chr6:4059376-4059686	A549	lung:	n/a	n/a
33	FOSL2	chr6:4059315-4059739	HepG2	liver:	n/a	chr6:4059690-4059699
34	JUND	chr6:4059430-4059656	HepG2	liver:	n/a	n/a
35	CTCF	chr6:4059440-4059590	NB4	blood:	n/a	n/a
36	CTCF	chr6:4059460-4059610	NHLF	lung:	n/a	n/a
37	CTCF	chr6:4059440-4059590	HCPEpiC	choroid plexus:	n/a	n/a
38	CTCF	chr6:4059420-4059570	HVMF	connective:	n/a	n/a
39	MAZ	chr6:4059414-4059760	K562	blood:	n/a	n/a
40	ZMIZ1	chr6:4059527-4059727	K562	blood:	n/a	n/a
41	FOSL2	chr6:4059260-4059842	HepG2	liver:	n/a	chr6:4059690-4059699
42	CTCF	chr6:4059460-4059610	HMEC	breast:	n/a	n/a
43	CTCF	chr6:4059460-4059610	HCPEpiC	choroid plexus:	n/a	n/a
44	POLR2A	chr6:4059373-4059721	MCF10A-Er-Src	breast:	n/a	n/a
45	STAT3	chr6:4059361-4059708	MCF10A-Er-Src	breast:	n/a	n/a
46	TAF1	chr6:4059464-4059676	SK-N-SH	brain:	n/a	n/a
47	CTCF	chr6:4059420-4059570	HBMEC	blood vessel:	n/a	n/a
48	CTCF	chr6:4059500-4059650	HVMF	connective:	n/a	n/a
49	CTCF	chr6:4059440-4059590	HepG2	liver:	n/a	n/a
50	MYBL2	chr6:4059284-4059849	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:4040955..4045707-chr6:4056854..4061183,4	K562	blood:
2	chr6:4054760..4058464-chr6:4059155..4063115,3	K562	blood:

Variant related genes	Relation type
PRPF4B	TF binding region
ENSG00000112739	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs13437140	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17137510	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17137511	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17137515	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17137567	0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes]
rs35539914	0.85[AFR][1000 genomes]
rs73721502	0.87[AFR][1000 genomes]
rs73723404	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73723405	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9502111	1.00[ASW][hapmap];1.00[LWK][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9502115	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9502116	0.94[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9503895	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9503896	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9503898	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9503902	1.00[ASW][hapmap];1.00[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9503903	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9503904	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9503905	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9503908	1.00[ASW][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][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	nsv532020	chr6:3417520-4140257	Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv1022968	chr6:3862744-4272502	Enhancers Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv538106	chr6:3862744-4272502	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv1034223	chr6:4030708-4060347	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv462615	chr6:4052383-4096678	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv600860	chr6:4052383-4096678	Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4023000-4063600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:4023200-4064000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr6:4023400-4071600	Weak transcription	Stomach Mucosa	stomach
4	chr6:4023800-4067000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:4030600-4065800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
6	chr6:4030800-4066600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr6:4031000-4066400	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr6:4031200-4066600	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr6:4034000-4066800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr6:4035600-4063600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr6:4035600-4064200	Strong transcription	H1 Cell Line	embryonic stem cell
12	chr6:4035800-4064600	Strong transcription	Primary B cells from peripheral blood	blood
13	chr6:4035800-4065000	Strong transcription	Dnd41	blood
14	chr6:4035800-4066000	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr6:4035800-4066000	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr6:4035800-4066200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr6:4036000-4066600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr6:4036000-4066600	Strong transcription	Duodenum Mucosa	Duodenum
19	chr6:4037200-4066200	Strong transcription	Liver	Liver
20	chr6:4037400-4065800	Strong transcription	Placenta	Placenta
21	chr6:4037600-4066200	Strong transcription	Rectal Mucosa Donor 31	rectum
22	chr6:4037600-4066400	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr6:4038800-4066000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr6:4040800-4065400	Strong transcription	GM12878-XiMat	blood
25	chr6:4042000-4066400	Strong transcription	Adipose Nuclei	Adipose
26	chr6:4048200-4063600	Strong transcription	Left Ventricle	heart
27	chr6:4048200-4063600	Strong transcription	Thymus	Thymus
28	chr6:4048200-4064000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr6:4048200-4064600	Strong transcription	Fetal Intestine Large	intestine
30	chr6:4048200-4065800	Strong transcription	Fetal Muscle Leg	muscle
31	chr6:4048600-4063800	Strong transcription	H9 Cell Line	embryonic stem cell
32	chr6:4049800-4062800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr6:4050200-4059800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr6:4050200-4060200	Weak transcription	Spleen	Spleen
35	chr6:4052000-4067000	Strong transcription	Primary B cells from cord blood	blood
36	chr6:4052400-4067400	Weak transcription	Psoas Muscle	Psoas
37	chr6:4053600-4062400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr6:4056000-4061200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr6:4056000-4065600	Strong transcription	Fetal Kidney	kidney
40	chr6:4056200-4066600	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr6:4056400-4060000	Weak transcription	Fetal Heart	heart
42	chr6:4056400-4061400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr6:4056400-4064200	Strong transcription	Fetal Muscle Trunk	muscle
44	chr6:4056400-4066400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr6:4056600-4061400	Strong transcription	Colonic Mucosa	Colon
46	chr6:4056600-4062000	Strong transcription	Brain Hippocampus Middle	brain
47	chr6:4056600-4063000	Strong transcription	Brain Inferior Temporal Lobe	brain
48	chr6:4056600-4063200	Strong transcription	Sigmoid Colon	Sigmoid Colon
49	chr6:4056600-4063400	Strong transcription	Fetal Lung	lung
50	chr6:4056600-4064000	Strong transcription	Brain Anterior Caudate	brain

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