Variant report

Variant	rs9399468
Chromosome Location	chr6:144290519-144290520
allele	A/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	GATA1	chr6:144290240-144291233	PBDE	blood:	n/a	chr6:144291032-144291039 chr6:144291030-144291040 chr6:144291032-144291042 chr6:144291140-144291150
2	ATF2	chr6:144290155-144290533	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr6:144290227-144290526	H1-hESC	embryonic stem cell:	n/a	n/a
4	TEAD4	chr6:144290174-144290593	H1-hESC	embryonic stem cell:	n/a	n/a
5	TAL1	chr6:144290267-144290568	K562	blood:	n/a	n/a
6	EGR1	chr6:144290252-144290532	H1-hESC	embryonic stem cell:	n/a	n/a
7	SP1	chr6:144290153-144290608	H1-hESC	embryonic stem cell:	n/a	n/a
8	ZNF274	chr6:144290276-144290528	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr6:144290216-144290552	H1-hESC	embryonic stem cell:	n/a	n/a
10	ATF2	chr6:144290215-144290614	H1-hESC	embryonic stem cell:	n/a	n/a
11	SP1	chr6:144290156-144290539	H1-hESC	embryonic stem cell:	n/a	n/a
12	YY1	chr6:144290208-144290531	H1-hESC	embryonic stem cell:	n/a	n/a
13	HDAC2	chr6:144290188-144290618	H1-hESC	embryonic stem cell:	n/a	n/a
14	TEAD4	chr6:144290173-144290628	K562	blood:	n/a	n/a
15	EP300	chr6:144290192-144290562	H1-hESC	embryonic stem cell:	n/a	n/a
16	TEAD4	chr6:144290079-144290620	H1-hESC	embryonic stem cell:	n/a	n/a
17	TEAD4	chr6:144290217-144290567	K562	blood:	n/a	n/a
18	TCF12	chr6:144290148-144290590	H1-hESC	embryonic stem cell:	n/a	n/a
19	TCF12	chr6:144290044-144290725	H1-hESC	embryonic stem cell:	n/a	n/a
20	MYC	chr6:144290364-144290519	K562	blood:	n/a	n/a

Variant related genes	Relation type
PLAGL1	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs2092894	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2224152	0.93[CEU][hapmap];0.87[EUR][1000 genomes]
rs2268448	0.86[EUR][1000 genomes]
rs6570599	0.86[CHB][hapmap]
rs9321953	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs9321956	0.93[EUR][1000 genomes]
rs9373409	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs9386053	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9390147	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs9390148	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs9390150	0.93[CEU][hapmap];0.93[EUR][1000 genomes]
rs9399469	0.86[CHB][hapmap];0.82[AFR][1000 genomes]
rs9403540	1.00[CEU][hapmap];0.90[EUR][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	esv3408554	chr6:144106707-144369589	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	esv3522138	chr6:144174685-144367463	Enhancers Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	esv3522139	chr6:144174685-144367463	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv830830	chr6:144177942-144380870	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:144269600-144294000	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr6:144269800-144296000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr6:144269800-144304400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr6:144271400-144296800	Weak transcription	Primary B cells from cord blood	blood
5	chr6:144275000-144293000	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr6:144277200-144291200	Genic enhancers	Fetal Muscle Leg	muscle
7	chr6:144280400-144291400	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr6:144281800-144294800	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr6:144284600-144290600	Weak transcription	Primary B cells from peripheral blood	blood
10	chr6:144284800-144294400	Weak transcription	Fetal Brain Male	brain
11	chr6:144284800-144318400	Weak transcription	Aorta	Aorta
12	chr6:144285000-144292400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr6:144285400-144291400	Weak transcription	Colonic Mucosa	Colon
14	chr6:144285400-144294200	Weak transcription	Left Ventricle	heart
15	chr6:144285800-144293400	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr6:144286800-144294200	Weak transcription	Fetal Brain Female	brain
17	chr6:144287000-144290600	Strong transcription	Fetal Muscle Trunk	muscle
18	chr6:144287000-144293000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr6:144287000-144294400	Weak transcription	Lung	lung
20	chr6:144287000-144294800	Weak transcription	Spleen	Spleen
21	chr6:144287000-144298800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr6:144287200-144290800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr6:144287200-144293000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr6:144287200-144293200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr6:144287200-144293400	Weak transcription	Fetal Intestine Small	intestine
26	chr6:144287400-144291000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr6:144287400-144294600	Enhancers	Adipose Nuclei	Adipose
28	chr6:144287600-144297600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr6:144287800-144292600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr6:144288200-144293400	Weak transcription	NHDF-Ad	bronchial
31	chr6:144288400-144291000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr6:144288400-144314800	Weak transcription	Primary hematopoietic stem cells	blood
33	chr6:144289000-144291800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr6:144289000-144295000	Enhancers	Fetal Lung	lung
35	chr6:144289000-144301800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr6:144289200-144293400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr6:144289400-144290600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
38	chr6:144289400-144290800	Weak transcription	Osteobl	bone
39	chr6:144289400-144294200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr6:144289800-144291200	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr6:144289800-144291200	Enhancers	Ovary	ovary
42	chr6:144289800-144292400	Enhancers	K562	blood
43	chr6:144289800-144292800	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr6:144289800-144293200	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr6:144290000-144291000	Weak transcription	Fetal Stomach	stomach
46	chr6:144290000-144294400	Weak transcription	Small Intestine	intestine
47	chr6:144290000-144296200	Weak transcription	NHLF	lung
48	chr6:144290200-144290800	Weak transcription	Placenta	Placenta
49	chr6:144290200-144290800	Enhancers	Fetal Thymus	thymus
50	chr6:144290200-144291800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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