Variant report

Variant	rs6809467
Chromosome Location	chr3:112362237-112362238
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	RAD21	chr3:112361707-112362298	A549	lung:	n/a	chr3:112361927-112361946
2	BCL3	chr3:112361629-112362254	A549	lung:	n/a	n/a
3	SP1	chr3:112361599-112362345	A549	lung:	n/a	chr3:112362012-112362025
4	RAD21	chr3:112361530-112362668	IMR90	lung:	n/a	chr3:112361927-112361946
5	EP300	chr3:112361556-112362839	A549	lung:	n/a	chr3:112361594-112361603
6	SIX5	chr3:112361457-112362455	A549	lung:	n/a	n/a
7	RAD21	chr3:112361666-112362254	SK-N-SH_RA	brain:	n/a	chr3:112361927-112361946
8	CTCF	chr3:112361227-112362721	A549	lung:	n/a	chr3:112361926-112361944 chr3:112361931-112361941 chr3:112361927-112361943 chr3:112361928-112361949
9	RAD21	chr3:112361630-112362239	ECC-1	luminal epithelium:	n/a	chr3:112361927-112361946
10	RAD21	chr3:112361595-112362401	A549	lung:	n/a	chr3:112361927-112361946
11	SP1	chr3:112361615-112362334	A549	lung:	n/a	chr3:112362012-112362025
12	CTCF	chr3:112361525-112362481	HCT-116	colon:	n/a	chr3:112361926-112361944 chr3:112361931-112361941 chr3:112361927-112361943 chr3:112361928-112361949
13	RAD21	chr3:112361637-112362247	MCF-7	breast:	n/a	chr3:112361927-112361946
14	TCF12	chr3:112361690-112362240	A549	lung:	n/a	n/a
15	RAD21	chr3:112361429-112362566	SK-N-SH	brain:	n/a	chr3:112361927-112361946
16	MAX	chr3:112361541-112363802	A549	lung:	n/a	n/a
17	EP300	chr3:112361626-112362318	A549	lung:	n/a	n/a
18	GATA3	chr3:112361558-112362604	A549	lung:	n/a	chr3:112362500-112362510
19	RAD21	chr3:112361496-112362381	HCT-116	colon:	n/a	chr3:112361927-112361946
20	RAD21	chr3:112361524-112362575	A549	lung:	n/a	chr3:112361927-112361946
21	RAD21	chr3:112361615-112362248	MCF-7	breast:	n/a	chr3:112361927-112361946
22	REST	chr3:112361764-112362696	A549	lung:	n/a	chr3:112362341-112362354
23	CTCF	chr3:112360993-112362408	SK-N-SH	brain:	n/a	chr3:112361926-112361944 chr3:112361931-112361941 chr3:112361927-112361943 chr3:112361928-112361949
24	SMC3	chr3:112361659-112362252	Hela-S3	cervix:	n/a	chr3:112361928-112361942
25	TCF12	chr3:112361493-112362934	A549	lung:	n/a	n/a
26	RAD21	chr3:112361591-112362257	ECC-1	luminal epithelium:	n/a	chr3:112361927-112361946
27	FOSL2	chr3:112361544-112362507	A549	lung:	n/a	chr3:112361592-112361601
28	SMC3	chr3:112361432-112362736	SK-N-SH	brain:	n/a	chr3:112361928-112361942
29	RAD21	chr3:112361574-112362261	HCT-116	colon:	n/a	chr3:112361927-112361946
30	SMC3	chr3:112361685-112362488	GM12878	blood:	n/a	chr3:112361928-112361942
31	CTCF	chr3:112361647-112362265	HCT-116	colon:	n/a	chr3:112361926-112361944 chr3:112361931-112361941 chr3:112361927-112361943 chr3:112361928-112361949
32	MAX	chr3:112361641-112362361	A549	lung:	n/a	n/a
33	CTCF	chr3:112361681-112362255	K562	blood:	n/a	chr3:112361926-112361944 chr3:112361931-112361941 chr3:112361927-112361943 chr3:112361928-112361949
34	POLR2A	chr3:112361724-112362237	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:112361784..112364489-chr3:112737772..112739628,2	MCF-7	breast:
2	chr3:112362227..112366265-chr3:112408651..112412487,6	MCF-7	breast:
3	chr3:112361852..112362399-chr3:112449227..112449774,2	MCF-7	breast:
4	chr3:112361475..112362409-chr3:112690827..112691683,2	MCF-7	breast:
5	chr3:112357856..112364091-chr3:112692717..112699765,9	MCF-7	breast:
6	chr3:112358506..112363260-chr3:112706755..112711649,8	K562	blood:
7	chr3:112361525..112362326-chr3:112533114..112533631,2	MCF-7	breast:
8	chr3:112361571..112362571-chr3:112533058..112533791,3	K562	blood:
9	chr3:112361676..112362437-chr3:112532636..112533651,5	MCF-7	breast:
10	chr3:112361572..112365675-chr3:112707892..112711353,4	MCF-7	breast:
11	chr3:112361482..112362387-chr3:112697930..112698730,3	MCF-7	breast:
12	chr3:112357488..112363507-chr3:112707947..112711649,7	K562	blood:
13	chr3:112361452..112362450-chr3:112697822..112699380,8	MCF-7	breast:
14	chr3:112279230..112281440-chr3:112358030..112362501,6	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CCDC80-1	chr3:112362185-112362304	XLOC_003217
2	lnc-CCDC80-1	chr3:112362109-112362304	NONHSAT091192
3	lnc-CCDC80-1	chr3:112362109-112362304	NONHSAT091191

Variant related genes	Relation type
CCDC80	TF binding region
ENSG00000144848	Chromatin interaction
ENSG00000138459	Chromatin interaction
ENSG00000272844	Chromatin interaction
ENSG00000163607	Chromatin interaction
ENSG00000163606	Chromatin interaction
ENSG00000240057	Chromatin interaction
ENSG00000163608	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1154272	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs1249913	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs1398092	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs1488263	1.00[YRI][hapmap]
rs2705540	1.00[YRI][hapmap]
rs2931761	1.00[YRI][hapmap]
rs4682113	1.00[AFR][1000 genomes]
rs7373716	1.00[AFR][1000 genomes]
rs7624745	1.00[AFR][1000 genomes]
rs820570	1.00[AFR][1000 genomes]
rs981180	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs981182	1.00[YRI][hapmap];0.90[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3329419	chr3:112236688-112620544	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS 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 miRNA target site	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112358600-112363200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr3:112358600-112365400	Weak transcription	Lung	lung
3	chr3:112358800-112363200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:112359000-112363600	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr3:112359400-112363200	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr3:112359600-112362800	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr3:112359600-112365400	Weak transcription	Pancreas	Pancrea
8	chr3:112359800-112362600	Weak transcription	Esophagus	oesophagus
9	chr3:112359800-112362800	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr3:112359800-112363000	Enhancers	HMEC	breast
11	chr3:112359800-112363400	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr3:112360200-112363600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr3:112360400-112362400	Enhancers	Fetal Stomach	stomach
14	chr3:112360600-112363000	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr3:112360600-112363400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr3:112360600-112363600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr3:112360600-112363800	Enhancers	Placenta Amnion	Placenta Amnion
18	chr3:112360800-112363400	Enhancers	HSMM	muscle
19	chr3:112360800-112365200	Weak transcription	Psoas Muscle	Psoas
20	chr3:112360800-112365600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr3:112360800-112367800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr3:112361000-112362400	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr3:112361000-112362400	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr3:112361000-112362600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr3:112361000-112362600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr3:112361000-112363200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:112361000-112363400	Enhancers	Muscle Satellite Cultured Cells	--
28	chr3:112361000-112365200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr3:112361000-112365800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr3:112361200-112363600	Enhancers	NHLF	lung
31	chr3:112361600-112362400	Active TSS	Brain Hippocampus Middle	brain
32	chr3:112361600-112362400	Enhancers	Fetal Heart	heart
33	chr3:112361600-112362600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr3:112361600-112362800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:112361600-112362800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr3:112361600-112362800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr3:112361600-112363200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr3:112361800-112362400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr3:112361800-112362400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr3:112361800-112362400	Enhancers	Fetal Muscle Leg	muscle
41	chr3:112361800-112362600	Enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr3:112361800-112362800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr3:112361800-112363000	Enhancers	Duodenum Smooth Muscle	Duodenum
44	chr3:112361800-112363600	Enhancers	Primary T cells fromperipheralblood	blood
45	chr3:112361800-112363800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
46	chr3:112362000-112362400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
47	chr3:112362000-112362400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr3:112362000-112362400	Enhancers	Primary hematopoietic stem cells	blood
49	chr3:112362000-112362400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
50	chr3:112362000-112362400	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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