Variant report

Variant	rs9496375
Chromosome Location	chr6:142739002-142739003
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:142733840..142736279-chr6:142738480..142740069,2	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs13437156	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1411147	1.00[AMR][1000 genomes]
rs6921559	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6939432	1.00[MEX][hapmap]
rs7760219	0.95[AFR][1000 genomes]
rs9484627	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9484628	1.00[AMR][1000 genomes]
rs9484629	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9484634	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9484635	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9484636	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9484638	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9484640	1.00[ASW][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9484641	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9484644	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9496336	1.00[AMR][1000 genomes]
rs9496350	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9496351	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9496359	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9496362	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9496363	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9496376	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9496381	1.00[ASW][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9496383	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9496384	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9496385	1.00[AMR][1000 genomes]
rs9496386	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9496387	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9496393	1.00[AMR][1000 genomes]
rs9496407	1.00[AMR][1000 genomes]
rs9496408	1.00[AMR][1000 genomes]
rs9496410	1.00[AMR][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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9496375	UGT2B17	trans	lymphoblastoid	seeQTL

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:142718000-142763200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr6:142721600-142749200	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr6:142722000-142743400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr6:142727000-142743400	Strong transcription	HepG2	liver
5	chr6:142729200-142743200	Strong transcription	Liver	Liver
6	chr6:142730200-142747600	Weak transcription	Fetal Intestine Small	intestine
7	chr6:142733400-142739200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr6:142733400-142739200	Enhancers	Osteobl	bone
9	chr6:142733800-142758000	Weak transcription	Stomach Smooth Muscle	stomach
10	chr6:142734200-142739200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr6:142734800-142743200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr6:142735200-142760200	Weak transcription	Esophagus	oesophagus
13	chr6:142735200-142765400	Weak transcription	Hela-S3	cervix
14	chr6:142735600-142743600	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr6:142735800-142740200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr6:142735800-142765400	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr6:142736800-142739200	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr6:142736800-142739200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr6:142736800-142739200	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr6:142736800-142743200	Strong transcription	Placenta	Placenta
21	chr6:142737400-142742200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr6:142737600-142741000	Weak transcription	Fetal Intestine Large	intestine
23	chr6:142737600-142765600	Weak transcription	Duodenum Mucosa	Duodenum
24	chr6:142737800-142765800	Weak transcription	Fetal Brain Male	brain
25	chr6:142738000-142739200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr6:142738000-142739200	Enhancers	Muscle Satellite Cultured Cells	--
27	chr6:142738000-142740200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr6:142738000-142774200	Weak transcription	NHEK	skin
29	chr6:142738200-142741200	Weak transcription	HMEC	breast
30	chr6:142738200-142743200	Strong transcription	Primary hematopoietic stem cells	blood
31	chr6:142738400-142741400	Strong transcription	A549	lung
32	chr6:142738400-142741600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr6:142738600-142740000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr6:142738600-142742200	Strong transcription	HUVEC	blood vessel
35	chr6:142738600-142742800	Weak transcription	NHDF-Ad	bronchial
36	chr6:142738800-142742000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr6:142738800-142743400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr6:142738800-142749600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr6:142739000-142740200	Weak transcription	Fetal Lung	lung
40	chr6:142739000-142741000	Weak transcription	HSMM	muscle
41	chr6:142739000-142741400	Weak transcription	HSMMtube	muscle
42	chr6:142739000-142741600	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr6:142739000-142742000	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr6:142739000-142742200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr6:142739000-142764800	Weak transcription	NHLF	lung

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