Variant report

Variant	rs9289125
Chromosome Location	chr3:118938621-118938622
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:118938238..118941184-chr3:118954679..118957762,3	K562	blood:
2	chr3:118936929..118943025-chr3:118955744..118960820,7	K562	blood:
3	chr3:118924439..118927161-chr3:118936255..118939127,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000121578	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10511384	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12690556	0.91[ASN][1000 genomes]
rs12695382	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12695383	0.97[ASN][1000 genomes]
rs13070981	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13091429	0.97[ASN][1000 genomes]
rs13094747	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13098659	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2001286	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28587867	0.89[ASN][1000 genomes]
rs28668839	0.93[ASN][1000 genomes]
rs28885082	0.91[ASN][1000 genomes]
rs35816234	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3752376	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3752377	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3796358	0.94[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57446248	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59140322	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59448071	0.97[ASN][1000 genomes]
rs6438503	1.00[CEU][hapmap]
rs68103027	0.88[ASN][1000 genomes]
rs71325367	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7650288	0.99[ASN][1000 genomes]
rs9812715	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9818595	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9824387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9832248	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9834466	0.94[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9835060	0.88[CEU][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs9836230	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9837110	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9844382	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9849672	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9850349	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9857127	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9858124	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9862321	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9867379	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9869645	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9874573	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9878996	0.94[CEU][hapmap]
rs9879593	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9881379	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9881947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	esv18354	chr3:118855337-119000251	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv591362	chr3:118906442-118948155	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:118924400-118959000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:118924600-118945600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:118926200-118939400	Strong transcription	Rectal Mucosa Donor 29	rectum
4	chr3:118927000-118943200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr3:118927000-118952600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr3:118927000-118953800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr3:118927000-118953800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr3:118927200-118939800	Strong transcription	Liver	Liver
9	chr3:118927200-118943000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr3:118927200-118953800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr3:118927200-118955200	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr3:118927400-118941200	Strong transcription	Placenta	Placenta
13	chr3:118927400-118950200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr3:118927400-118953000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr3:118927600-118952400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr3:118927800-118939200	Strong transcription	Primary hematopoietic stem cells	blood
17	chr3:118927800-118940600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr3:118927800-118943400	Strong transcription	Fetal Muscle Trunk	muscle
19	chr3:118927800-118956400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr3:118928000-118943000	Strong transcription	Fetal Muscle Leg	muscle
21	chr3:118928000-118955600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr3:118928200-118939200	Strong transcription	Placenta Amnion	Placenta Amnion
23	chr3:118928200-118940000	Strong transcription	Brain Hippocampus Middle	brain
24	chr3:118928200-118943200	Strong transcription	Fetal Stomach	stomach
25	chr3:118928200-118943400	Strong transcription	Adipose Nuclei	Adipose
26	chr3:118928200-118951000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr3:118928400-118940200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr3:118928800-118950000	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr3:118929000-118939800	Strong transcription	Skeletal Muscle Female	skeletal muscle
30	chr3:118929000-118943000	Strong transcription	Skeletal Muscle Male	skeletal muscle
31	chr3:118929000-118943200	Strong transcription	Left Ventricle	heart
32	chr3:118929000-118943600	Strong transcription	Primary neutrophils fromperipheralblood	blood
33	chr3:118929000-118944200	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr3:118929200-118956200	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr3:118929200-118956200	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr3:118929200-118956400	Strong transcription	H1 Cell Line	embryonic stem cell
37	chr3:118929200-118956600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
38	chr3:118929400-118940200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr3:118929400-118943000	Strong transcription	H9 Cell Line	embryonic stem cell
40	chr3:118930000-118939000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr3:118930000-118940600	Strong transcription	Osteobl	bone
42	chr3:118930000-118943000	Strong transcription	Stomach Smooth Muscle	stomach
43	chr3:118930000-118943600	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr3:118930000-118949800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr3:118930000-118955400	Strong transcription	Primary B cells from peripheral blood	blood
46	chr3:118930200-118943600	Strong transcription	HMEC	breast
47	chr3:118930200-118955800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr3:118930200-118958400	Weak transcription	Hela-S3	cervix
49	chr3:118930400-118943400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr3:118930800-118942400	Strong transcription	Muscle Satellite Cultured Cells	--

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