Variant report

Variant	rs17481190
Chromosome Location	chr6:30743014-30743015
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:30742016..30748001-chr6:30748066..30750476,5	MCF-7	breast:
2	chr6:30648927..30651629-chr6:30742930..30745365,2	K562	blood:
3	chr6:30742999..30744721-chr6:30782116..30783840,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228022	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12526186	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12527188	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12660860	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12660883	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12662149	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13202739	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13214831	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13217914	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13220225	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17189441	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28670020	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28780111	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28780113	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28780114	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28780120	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28780121	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28780122	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28894082	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3869075	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4278006	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4713361	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	esv2758041	chr6:30644693-30816319	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
6	esv2759413	chr6:30644693-30816319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
7	nsv884100	chr6:30693816-30751326	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
8	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
9	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
10	nsv870418	chr6:30713196-30755668	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
11	nsv527226	chr6:30716719-30772378	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
12	nsv884103	chr6:30729487-30755668	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
13	nsv884104	chr6:30740680-30753146	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17481190	IP6K3	cis	parietal	SCAN
rs17481190	DDR1	cis	lymphoblastoid	seeQTL
rs17481190	ZNF192	cis	cerebellum	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30734800-30747400	Weak transcription	Liver	Liver
2	chr6:30737600-30744200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr6:30737600-30746000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr6:30737600-30746000	Weak transcription	Fetal Lung	lung
5	chr6:30737600-30746000	Weak transcription	Gastric	stomach
6	chr6:30737600-30746000	Weak transcription	Lung	lung
7	chr6:30737600-30746000	Weak transcription	Pancreas	Pancrea
8	chr6:30737600-30746000	Weak transcription	Right Atrium	heart
9	chr6:30737600-30746000	Weak transcription	Right Ventricle	heart
10	chr6:30737600-30746000	Weak transcription	Spleen	Spleen
11	chr6:30737600-30746200	Weak transcription	Psoas Muscle	Psoas
12	chr6:30737600-30746600	Weak transcription	Aorta	Aorta
13	chr6:30737600-30749200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr6:30738000-30746000	Weak transcription	Colon Smooth Muscle	Colon
15	chr6:30738000-30746400	Weak transcription	Esophagus	oesophagus
16	chr6:30738200-30745200	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr6:30738400-30747000	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr6:30738600-30745800	Weak transcription	NH-A	brain
19	chr6:30738600-30746000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr6:30738600-30746000	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr6:30738600-30747000	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr6:30738600-30749200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr6:30738800-30744600	Weak transcription	Fetal Thymus	thymus
24	chr6:30738800-30746200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr6:30738800-30746800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr6:30739000-30744000	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr6:30739000-30744200	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr6:30739000-30746000	Weak transcription	K562	blood
29	chr6:30740600-30746000	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr6:30740800-30744400	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr6:30741000-30746000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr6:30741000-30749600	Weak transcription	Thymus	Thymus
33	chr6:30742000-30743800	Enhancers	Fetal Heart	heart
34	chr6:30742000-30749000	Enhancers	HepG2	liver
35	chr6:30742200-30744400	Weak transcription	Primary T cells from cord blood	blood
36	chr6:30742200-30744800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr6:30742200-30746200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr6:30742400-30743200	Enhancers	Fetal Muscle Leg	muscle
39	chr6:30742400-30743200	Enhancers	Placenta	Placenta
40	chr6:30742400-30743200	Enhancers	Left Ventricle	heart
41	chr6:30742400-30743200	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr6:30742400-30743200	Enhancers	Stomach Smooth Muscle	stomach
43	chr6:30742400-30743200	Enhancers	NHDF-Ad	bronchial
44	chr6:30742400-30743400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr6:30742400-30743400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr6:30742400-30743400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr6:30742400-30743400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr6:30742400-30743400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr6:30742400-30746200	Enhancers	Hela-S3	cervix
50	chr6:30742600-30743200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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