Variant report

Variant	rs2394388
Chromosome Location	chr6:30599741-30599742
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	JUND	chr6:30599574-30599827	K562	blood:	n/a	n/a
2	FOS	chr6:30599553-30599820	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr6:30599554-30599780	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr6:30599678-30599754	MCF10A-Er-Src	breast:	n/a	n/a
5	MAFF	chr6:30599615-30599786	K562	blood:	n/a	n/a
6	FOS	chr6:30599554-30599828	MCF10A-Er-Src	breast:	n/a	n/a
7	FOSL2	chr6:30599505-30599891	SK-N-SH	brain:	n/a	n/a
8	MAFK	chr6:30599594-30599757	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:30455831..30458376-chr6:30599698..30601458,2	MCF-7	breast:
2	chr6:30598934..30603301-chr6:30608761..30613584,7	MCF-7	breast:
3	chr6:30594543..30596206-chr6:30598206..30601181,2	MCF-7	breast:

Variant related genes	Relation type
PTMAP1	TF binding region
ENSG00000204592	Chromatin interaction
ENSG00000137343	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs16867845	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17189120	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17189134	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17189155	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17195411	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17195474	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17195488	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17195516	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2106069	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2239514	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2239515	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2239516	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2267638	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2267640	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2302347	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2394387	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2394389	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3815101	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3888777	0.83[AMR][1000 genomes]
rs4148247	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57626358	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs58423891	0.90[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs58569354	0.90[AFR][1000 genomes]
rs59272830	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59607822	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59913575	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60081418	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60365864	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs60399658	0.88[ASN][1000 genomes]
rs61134417	0.90[AFR][1000 genomes]
rs61733213	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6457246	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6457247	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6457248	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6457249	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6899769	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6899862	0.94[ASN][1000 genomes]
rs6901251	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6911174	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6917434	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6917935	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6918007	0.97[AFR][1000 genomes]
rs6925437	0.82[AFR][1000 genomes]
rs6934466	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7742291	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7742650	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7742754	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7746096	0.90[AFR][1000 genomes]
rs7749109	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7749807	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7749978	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7767002	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7767714	0.90[AFR][1000 genomes]
rs7768140	0.90[AFR][1000 genomes]
rs7773711	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9262120	1.00[ASN][1000 genomes]
rs9468812	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9468821	0.82[ASN][1000 genomes]
rs9468822	0.82[ASN][1000 genomes]
rs9468823	0.82[ASN][1000 genomes]
rs9500865	0.82[ASN][1000 genomes]
rs9671	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025667	chr6:30292845-30638066	Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	825 gene(s)	inside rSNPs	diseases
2	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
4	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
5	esv3430377	chr6:30443802-30814426	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	967 gene(s)	inside rSNPs	diseases
6	nsv884086	chr6:30462084-30672757	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	798 gene(s)	inside rSNPs	diseases
7	nsv830626	chr6:30558064-30732905	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	406 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2394388	PRR3	cis	lymphoblastoid	seeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30593600-30613800	Weak transcription	Hela-S3	cervix
2	chr6:30595000-30601200	Weak transcription	Aorta	Aorta
3	chr6:30595200-30601000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:30595200-30601200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr6:30595200-30607000	Weak transcription	Right Atrium	heart
6	chr6:30595200-30609000	Weak transcription	Colonic Mucosa	Colon
7	chr6:30595400-30601400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr6:30595400-30607800	Weak transcription	Right Ventricle	heart
9	chr6:30595400-30608200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr6:30595400-30608400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr6:30595400-30614000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr6:30595400-30614800	Weak transcription	Small Intestine	intestine
13	chr6:30595600-30600800	Weak transcription	Colon Smooth Muscle	Colon
14	chr6:30595600-30600800	Weak transcription	Left Ventricle	heart
15	chr6:30595600-30600800	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr6:30595600-30601000	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr6:30595600-30601200	Weak transcription	Adipose Nuclei	Adipose
18	chr6:30595600-30601200	Weak transcription	Esophagus	oesophagus
19	chr6:30595600-30601200	Weak transcription	Gastric	stomach
20	chr6:30595600-30601200	Weak transcription	Rectal Smooth Muscle	rectum
21	chr6:30595600-30601200	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr6:30595600-30601200	Weak transcription	HMEC	breast
23	chr6:30595600-30601200	Weak transcription	NHDF-Ad	bronchial
24	chr6:30595600-30601400	Weak transcription	NH-A	brain
25	chr6:30595600-30605200	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr6:30595600-30608000	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr6:30595600-30608200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr6:30595600-30608600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr6:30595600-30611000	Weak transcription	Primary B cells from cord blood	blood
30	chr6:30595600-30613000	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr6:30595600-30613800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr6:30595600-30614200	Strong transcription	Fetal Muscle Trunk	muscle
33	chr6:30595600-30614200	Strong transcription	Fetal Stomach	stomach
34	chr6:30595600-30614200	Weak transcription	Psoas Muscle	Psoas
35	chr6:30595600-30614400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr6:30595800-30600200	Strong transcription	H1 Cell Line	embryonic stem cell
37	chr6:30595800-30600200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr6:30595800-30601000	Weak transcription	A549	lung
39	chr6:30595800-30601200	Weak transcription	Pancreas	Pancrea
40	chr6:30595800-30601200	Weak transcription	Stomach Mucosa	stomach
41	chr6:30595800-30601800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr6:30595800-30602000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr6:30595800-30602000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr6:30595800-30602000	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr6:30595800-30602200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr6:30595800-30602400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
47	chr6:30595800-30602400	Strong transcription	Fetal Intestine Large	intestine
48	chr6:30595800-30602400	Strong transcription	Fetal Thymus	thymus
49	chr6:30595800-30603200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr6:30595800-30604200	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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