Variant report

Variant	rs4076539
Chromosome Location	chr6:24803912-24803913
allele	A/C
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	ARID3A	chr6:24803165-24804029	HepG2	liver:	n/a	n/a
2	EP300	chr6:24803493-24803949	HepG2	liver:	n/a	n/a
3	EP300	chr6:24803513-24804064	HepG2	liver:	n/a	n/a
4	NR3C1	chr6:24803600-24804009	A549	lung:	n/a	n/a
5	MAFK	chr6:24803607-24803928	HepG2	liver:	n/a	chr6:24803755-24803765
6	JUND	chr6:24803619-24803990	HepG2	liver:	n/a	chr6:24803754-24803764 chr6:24803754-24803764 chr6:24803753-24803764 chr6:24803754-24803764 chr6:24803754-24803764
7	MAFF	chr6:24803626-24803957	HepG2	liver:	n/a	n/a
8	FOXA1	chr6:24803534-24804017	HepG2	liver:	n/a	chr6:24803550-24803562
9	HDAC2	chr6:24803085-24804018	HepG2	liver:	n/a	chr6:24803817-24803825
10	JUND	chr6:24803686-24803968	HepG2	liver:	n/a	chr6:24803754-24803764 chr6:24803754-24803764 chr6:24803753-24803764 chr6:24803754-24803764 chr6:24803754-24803764
11	MYBL2	chr6:24802985-24804101	HepG2	liver:	n/a	n/a
12	ZBTB7A	chr6:24803629-24803983	HepG2	liver:	n/a	n/a
13	FOXA1	chr6:24803120-24803982	A549	lung:	n/a	chr6:24803550-24803562
14	FOSL2	chr6:24803567-24803983	HepG2	liver:	n/a	chr6:24803754-24803764 chr6:24803754-24803764 chr6:24803754-24803764 chr6:24803754-24803764
15	JUN	chr6:24803632-24803936	HepG2	liver:	n/a	chr6:24803754-24803764 chr6:24803754-24803764 chr6:24803754-24803764 chr6:24803754-24803764
16	FOXA1	chr6:24803194-24804024	HepG2	liver:	n/a	chr6:24803550-24803562
17	FOXA2	chr6:24803091-24804231	HepG2	liver:	n/a	chr6:24803550-24803562
18	FOXA2	chr6:24803087-24803969	HepG2	liver:	n/a	chr6:24803550-24803562
19	FOXA1	chr6:24803080-24804053	HepG2	liver:	n/a	chr6:24803550-24803562
20	MBD4	chr6:24803152-24804070	HepG2	liver:	n/a	n/a
21	TEAD4	chr6:24802961-24804063	HepG2	liver:	n/a	n/a
22	RXRA	chr6:24803676-24803979	HepG2	liver:	n/a	n/a
23	EP300	chr6:24803681-24803994	HepG2	liver:	n/a	n/a
24	FOXA1	chr6:24803601-24804009	HepG2	liver:	n/a	n/a
25	FOSL2	chr6:24803561-24804045	HepG2	liver:	n/a	chr6:24803754-24803764 chr6:24803754-24803764 chr6:24803754-24803764 chr6:24803754-24803764
26	NFIC	chr6:24803027-24804072	HepG2	liver:	n/a	n/a
27	RCOR1	chr6:24803690-24803991	HepG2	liver:	n/a	n/a
28	NR3C1	chr6:24803670-24804001	A549	lung:	n/a	n/a

Variant related genes	Relation type
C6orf229	TF binding region

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs13202640	0.91[EUR][1000 genomes]
rs13209580	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4076540	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4078356	0.90[AMR][1000 genomes];0.99[EUR][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	nsv830609	chr6:24712086-24896647	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv1022966	chr6:24763776-25154212	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv538160	chr6:24763776-25154212	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv5227	chr6:24774149-24824012	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv508396	chr6:24779648-24846309	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24776400-24807400	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr6:24776800-24807600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr6:24777000-24805000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr6:24777000-24806200	Weak transcription	Spleen	Spleen
5	chr6:24777000-24808000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr6:24777000-24809400	Weak transcription	Brain Germinal Matrix	brain
7	chr6:24777000-24811600	Weak transcription	Brain Hippocampus Middle	brain
8	chr6:24777000-24847600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr6:24777000-24859600	Weak transcription	Psoas Muscle	Psoas
10	chr6:24787600-24806200	Weak transcription	Fetal Stomach	stomach
11	chr6:24788000-24805600	Weak transcription	Fetal Muscle Leg	muscle
12	chr6:24788000-24810200	Weak transcription	Left Ventricle	heart
13	chr6:24788000-24832000	Weak transcription	Brain Substantia Nigra	brain
14	chr6:24788800-24848200	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr6:24789000-24807000	Weak transcription	GM12878-XiMat	blood
16	chr6:24789200-24805800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr6:24789200-24807400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr6:24789200-24842600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr6:24789400-24807400	Weak transcription	Fetal Muscle Trunk	muscle
20	chr6:24789400-24807800	Weak transcription	Dnd41	blood
21	chr6:24798200-24827400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr6:24798200-24841200	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr6:24799400-24805000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr6:24799400-24805000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr6:24800000-24807400	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr6:24800000-24843200	Weak transcription	Liver	Liver
27	chr6:24800200-24806600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr6:24800200-24809400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr6:24800400-24821800	Weak transcription	Fetal Heart	heart
30	chr6:24800600-24806200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr6:24800800-24811800	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr6:24800800-24811800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr6:24801000-24812000	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr6:24801200-24811800	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr6:24801200-24812000	Strong transcription	Primary B cells from peripheral blood	blood
36	chr6:24801400-24811800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr6:24801600-24811200	Strong transcription	Primary T cells from cord blood	blood
38	chr6:24802000-24806400	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr6:24802000-24810600	Strong transcription	Primary B cells from cord blood	blood
40	chr6:24802000-24811000	Strong transcription	Primary hematopoietic stem cells	blood
41	chr6:24802000-24811000	Strong transcription	Fetal Thymus	thymus
42	chr6:24802000-24811600	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr6:24802000-24811800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr6:24802000-24811800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr6:24802000-24812000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr6:24802400-24804000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr6:24802400-24804200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr6:24802400-24811600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
49	chr6:24802400-24811600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr6:24802400-24811800	Strong transcription	Primary T helper cells PMA-I stimulated	--

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