Variant report

Variant	rs7753595
Chromosome Location	chr6:133086519-133086520
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:133084415..133087080-chr6:133134762..133137402,2	MCF-7	breast:
2	chr6:133054047..133059196-chr6:133082600..133087082,5	MCF-7	breast:
3	chr6:133084618..133086907-chr6:133118822..133121566,2	K562	blood:
4	chr6:133084942..133087324-chr6:133134860..133137280,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RPS12-3	chr6:133085799-133086597	NONHSAT114973

Variant related genes	Relation type
ENSG00000112306	Chromatin interaction
ENSG00000146409	Chromatin interaction
ENSG00000093134	Chromatin interaction
ENSG00000206754	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1122175	1.00[JPT][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11964512	0.90[AFR][1000 genomes]
rs11965927	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12211701	0.81[YRI][hapmap]
rs1467403	0.85[YRI][hapmap];0.90[AFR][1000 genomes]
rs1467404	0.84[ASW][hapmap];0.96[LWK][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes]
rs34688576	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34934410	1.00[ASN][1000 genomes]
rs35148730	1.00[ASN][1000 genomes]
rs3736725	1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756971	1.00[ASN][1000 genomes]
rs41286184	1.00[ASN][1000 genomes]
rs56908272	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57176306	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58949949	0.81[ASN][1000 genomes]
rs59357932	0.91[ASN][1000 genomes]
rs59716502	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59718818	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60133731	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60177375	0.91[ASN][1000 genomes]
rs60631157	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61310652	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6569847	0.85[YRI][hapmap]
rs6569851	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6569852	1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6905784	1.00[ASN][1000 genomes]
rs6911773	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6924403	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6926101	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6927991	1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6928237	1.00[ASN][1000 genomes]
rs6928933	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6930549	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6930703	1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6934155	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6934161	0.81[LWK][hapmap];0.81[YRI][hapmap]
rs6934190	1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73547611	0.81[ASN][1000 genomes]
rs73550455	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73554461	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73558375	0.91[ASN][1000 genomes]
rs73558378	0.91[ASN][1000 genomes]
rs73558387	0.91[ASN][1000 genomes]
rs7738256	1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7738569	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7744961	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7747544	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7748090	0.91[ASN][1000 genomes]
rs7759524	1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7761207	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7762248	1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7769354	0.91[ASN][1000 genomes]
rs7770081	0.84[ASW][hapmap];0.91[LWK][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes]
rs7775241	1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9321369	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9321370	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9321375	1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9483501	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9483502	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9493434	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9493435	0.84[ASW][hapmap];0.91[LWK][hapmap];0.81[YRI][hapmap];0.90[AFR][1000 genomes]
rs9493437	0.87[AFR][1000 genomes]
rs9493440	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9493441	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9493445	0.81[YRI][hapmap]
rs9493446	0.81[LWK][hapmap];0.81[YRI][hapmap]
rs9493447	1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9493449	1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9493455	0.91[ASN][1000 genomes]
rs9493457	0.91[ASN][1000 genomes]
rs9766095	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9767075	0.91[EUR][1000 genomes];1.00[ASN][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	nsv532069	chr6:132776411-133462292	Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv1015742	chr6:132933666-133285852	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7753595	C6orf192	cis	multi-tissue	Pritchard

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:133061400-133098000	Weak transcription	Spleen	Spleen
2	chr6:133065000-133098000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr6:133081400-133096800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr6:133081800-133086800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr6:133083200-133086600	Enhancers	Fetal Intestine Large	intestine
6	chr6:133083400-133090600	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr6:133083600-133099000	Weak transcription	Left Ventricle	heart
8	chr6:133083800-133118200	Weak transcription	Brain Cingulate Gyrus	brain
9	chr6:133084000-133089000	Weak transcription	Fetal Intestine Small	intestine
10	chr6:133084600-133087000	Enhancers	Fetal Stomach	stomach
11	chr6:133084600-133091200	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr6:133084800-133089400	Weak transcription	Fetal Thymus	thymus
13	chr6:133084800-133091800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr6:133084800-133097000	Weak transcription	Fetal Muscle Leg	muscle
15	chr6:133085000-133086600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr6:133085000-133086600	Enhancers	NHDF-Ad	bronchial
17	chr6:133085000-133109000	Weak transcription	GM12878-XiMat	blood
18	chr6:133085000-133114600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr6:133085000-133119000	Weak transcription	Thymus	Thymus
20	chr6:133085200-133086600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr6:133085200-133089800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr6:133085200-133090000	Weak transcription	Primary B cells from cord blood	blood
23	chr6:133085200-133112200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr6:133085200-133119400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr6:133085400-133089000	Weak transcription	Primary B cells from peripheral blood	blood
26	chr6:133085400-133089200	Weak transcription	Liver	Liver
27	chr6:133085400-133090000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr6:133085400-133091200	Weak transcription	Primary T cells from cord blood	blood
29	chr6:133085400-133091200	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr6:133085400-133114400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr6:133085600-133088200	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr6:133085600-133089000	Weak transcription	Stomach Mucosa	stomach
33	chr6:133085600-133090400	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr6:133085600-133090800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr6:133085600-133098800	Weak transcription	Brain Hippocampus Middle	brain
36	chr6:133085600-133099800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr6:133085600-133118800	Weak transcription	Colon Smooth Muscle	Colon
38	chr6:133085800-133088800	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr6:133085800-133089000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr6:133085800-133089000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr6:133085800-133089200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr6:133085800-133089200	Weak transcription	Lung	lung
43	chr6:133085800-133090000	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr6:133085800-133091000	Weak transcription	Fetal Lung	lung
45	chr6:133085800-133091200	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr6:133085800-133091200	Weak transcription	Placenta	Placenta
47	chr6:133085800-133091200	Weak transcription	Ovary	ovary
48	chr6:133085800-133093200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr6:133085800-133100000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr6:133085800-133100000	Weak transcription	Aorta	Aorta

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