Variant report

Variant	rs9365133
Chromosome Location	chr6:160531775-160531776
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	chr6:160524963..160527008-chr6:160529525..160532006,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC22A1-2	chr6:160529406-160532536	ENSG00000270949.1

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1050015	0.83[TSI][hapmap];0.82[AFR][1000 genomes]
rs1479355	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1867350	0.84[CHD][hapmap];1.00[JPT][hapmap]
rs1867351	1.00[CEU][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1871388	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2297366	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2297370	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2297371	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2297372	0.85[CEU][hapmap]
rs3798168	0.84[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs3798169	0.84[ASN][1000 genomes]
rs3798173	0.89[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.97[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3822841	1.00[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap]
rs4551194	0.81[ASN][1000 genomes]
rs4646273	0.86[ASN][1000 genomes]
rs4646274	0.85[ASN][1000 genomes]
rs4709399	0.83[CEU][hapmap]
rs4709400	1.00[CEU][hapmap];0.82[AMR][1000 genomes]
rs56384560	0.82[AFR][1000 genomes]
rs58458113	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6935207	1.00[CEU][hapmap];0.82[AMR][1000 genomes]
rs73025542	0.80[AFR][1000 genomes]
rs755883	0.87[ASN][1000 genomes]
rs755884	0.84[CEU][hapmap]
rs7746102	0.91[MEX][hapmap]
rs7753051	0.92[EUR][1000 genomes]
rs7760552	0.80[CEU][hapmap];0.82[MEX][hapmap]
rs7769472	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9346808	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9347385	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9355776	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9365131	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9365132	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758089	chr6:160372244-161234665	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	esv2759484	chr6:160372244-161234665	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	esv35098	chr6:160422589-161070870	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	esv2757197	chr6:160432331-161070870	Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv818463	chr6:160435569-161025547	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9365133	OSTCL	cis	parietal	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:160453000-160534600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr6:160455800-160532000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr6:160464600-160531800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr6:160511400-160532600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr6:160512000-160532800	Weak transcription	A549	lung
6	chr6:160512000-160539200	Weak transcription	Stomach Mucosa	stomach
7	chr6:160518000-160532200	Weak transcription	Fetal Brain Male	brain
8	chr6:160521800-160537600	Strong transcription	Fetal Intestine Small	intestine
9	chr6:160522400-160532000	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr6:160522800-160532200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr6:160523200-160540200	Weak transcription	Fetal Heart	heart
12	chr6:160526200-160539000	Weak transcription	Colon Smooth Muscle	Colon
13	chr6:160526200-160548600	Weak transcription	K562	blood
14	chr6:160526400-160533400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr6:160526400-160536800	Weak transcription	Primary B cells from peripheral blood	blood
16	chr6:160526800-160531800	Weak transcription	Hela-S3	cervix
17	chr6:160526800-160532000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr6:160526800-160532600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr6:160526800-160532800	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr6:160526800-160532800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr6:160526800-160533000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr6:160526800-160533000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr6:160526800-160533000	Weak transcription	Fetal Brain Female	brain
24	chr6:160526800-160537000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr6:160526800-160538600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr6:160526800-160540600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr6:160526800-160545000	Weak transcription	HMEC	breast
28	chr6:160527000-160532000	Weak transcription	Brain Germinal Matrix	brain
29	chr6:160527000-160532600	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr6:160527000-160532800	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr6:160527000-160538800	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr6:160527000-160545000	Weak transcription	NHDF-Ad	bronchial
33	chr6:160527200-160541200	Weak transcription	Osteobl	bone
34	chr6:160527400-160533200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr6:160527400-160538400	Weak transcription	Brain Cingulate Gyrus	brain
36	chr6:160527400-160538800	Weak transcription	Brain Hippocampus Middle	brain
37	chr6:160527400-160549200	Weak transcription	Colonic Mucosa	Colon
38	chr6:160527400-160550000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr6:160527600-160541200	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr6:160527800-160538000	Weak transcription	Gastric	stomach
41	chr6:160528000-160538000	Weak transcription	Liver	Liver
42	chr6:160528000-160538400	Weak transcription	Ovary	ovary
43	chr6:160528600-160532600	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr6:160528600-160538000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr6:160528800-160535800	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr6:160529000-160533000	Weak transcription	NH-A	brain
47	chr6:160529000-160539600	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr6:160529200-160533600	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr6:160529200-160538000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr6:160529200-160538200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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