Variant report

Variant	rs9389990
Chromosome Location	chr6:142707419-142707420
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:142621714..142625122-chr6:142706932..142708951,3	MCF-7	breast:
2	chr6:142616281..142618889-chr6:142707145..142709982,2	MCF-7	breast:
3	chr6:142695789..142698729-chr6:142704783..142708780,4	MCF-7	breast:
4	chr6:142622324..142625256-chr6:142705073..142708395,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112414	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1013902	1.00[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17071798	0.88[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2064314	0.88[CEU][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2143390	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2223616	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2294765	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2294768	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2294770	0.88[CEU][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2294772	0.88[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2294773	0.88[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2294774	0.88[CEU][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34701089	0.86[EUR][1000 genomes]
rs41289839	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4140531	1.00[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6570512	0.88[CEU][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6913116	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7758750	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7759268	0.88[CEU][hapmap];0.82[CHB][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9321865	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9321871	0.83[EUR][1000 genomes]
rs9373343	1.00[CEU][hapmap];0.84[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9373345	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9376687	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9376689	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9385993	0.88[CEU][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9385994	0.88[CEU][hapmap];0.88[CHB][hapmap];0.83[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9389988	0.82[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9403379	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9403384	0.88[CEU][hapmap];0.83[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9484645	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949088	chr6:142561402-143128849	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv830825	chr6:142585242-142752575	Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:142698600-142733200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr6:142698800-142707600	Weak transcription	Placenta	Placenta
3	chr6:142698800-142707800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:142699600-142708000	Weak transcription	Pancreas	Pancrea
5	chr6:142699600-142709200	Weak transcription	Fetal Intestine Large	intestine
6	chr6:142699800-142708000	Weak transcription	Liver	Liver
7	chr6:142699800-142709000	Weak transcription	Fetal Intestine Small	intestine
8	chr6:142699800-142718600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr6:142699800-142719200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr6:142700000-142714200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr6:142700400-142709000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr6:142700400-142709000	Weak transcription	Fetal Lung	lung
13	chr6:142702200-142707800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr6:142703200-142708200	Strong transcription	HUVEC	blood vessel
15	chr6:142705800-142713800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr6:142706200-142719600	Weak transcription	NHEK	skin
17	chr6:142706400-142709000	Weak transcription	Primary hematopoietic stem cells	blood
18	chr6:142706400-142709200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr6:142706400-142717200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr6:142706600-142707800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr6:142706600-142707800	Strong transcription	HepG2	liver
22	chr6:142706600-142709600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr6:142706600-142709600	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr6:142706600-142710200	Enhancers	A549	lung
25	chr6:142706800-142708200	Weak transcription	Hela-S3	cervix
26	chr6:142706800-142708200	Weak transcription	NHLF	lung
27	chr6:142706800-142709800	Weak transcription	HSMM	muscle
28	chr6:142707000-142709200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr6:142707400-142708800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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