Variant report

Variant	rs4960955
Chromosome Location	chr8:87120742-87120743
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:87118812..87121413-chr8:87301706..87304462,2	MCF-7	breast:
2	chr8:87119574..87121153-chr8:87526480..87528203,2	MCF-7	breast:
3	chr8:87120472..87122608-chr8:87135195..87138128,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000176623	Chromatin interaction
ENSG00000085719	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10097379	0.81[JPT][hapmap]
rs10098631	0.87[CHB][hapmap];0.91[JPT][hapmap];0.82[YRI][hapmap];0.89[ASN][1000 genomes]
rs10099368	0.87[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs10101407	0.88[ASN][1000 genomes]
rs10102252	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10103166	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10106391	0.87[CHB][hapmap];0.91[JPT][hapmap];0.82[YRI][hapmap];0.89[ASN][1000 genomes]
rs10106497	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10112076	0.87[CHB][hapmap];0.91[JPT][hapmap];0.82[YRI][hapmap];0.89[ASN][1000 genomes]
rs10504819	0.87[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10955870	0.81[ASN][1000 genomes]
rs11988449	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs12156049	0.83[CHB][hapmap]
rs12677162	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12682430	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs13252217	0.83[CHB][hapmap]
rs13254996	0.81[JPT][hapmap]
rs13257877	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13260768	0.89[ASN][1000 genomes]
rs13267067	0.87[CHB][hapmap];0.91[JPT][hapmap];0.82[YRI][hapmap];0.84[ASN][1000 genomes]
rs13274057	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13281890	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1351777	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1384877	0.83[CHB][hapmap]
rs1384878	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1384879	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1483765	0.87[ASN][1000 genomes]
rs1601151	0.83[CHB][hapmap]
rs16876450	0.83[CHB][hapmap]
rs16881545	0.95[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs16883602	1.00[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs16887456	0.87[CHB][hapmap];0.91[JPT][hapmap];0.90[LWK][hapmap];0.82[YRI][hapmap];0.89[ASN][1000 genomes]
rs1872135	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs1968869	0.87[ASN][1000 genomes]
rs2220106	0.87[ASN][1000 genomes]
rs2318396	0.87[CHB][hapmap];0.91[JPT][hapmap];0.90[LWK][hapmap];0.82[YRI][hapmap];0.88[ASN][1000 genomes]
rs2318936	0.87[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs2626333	0.81[JPT][hapmap]
rs2626337	0.81[JPT][hapmap]
rs2626338	0.81[JPT][hapmap]
rs2626341	0.81[JPT][hapmap]
rs2626343	0.81[JPT][hapmap]
rs2721248	0.81[JPT][hapmap]
rs2721252	0.81[JPT][hapmap]
rs2721255	0.81[JPT][hapmap]
rs28415682	0.89[ASN][1000 genomes]
rs2873692	0.89[ASN][1000 genomes]
rs35216834	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35910910	0.94[ASN][1000 genomes]
rs3802225	0.83[CHB][hapmap]
rs4370510	0.85[ASN][1000 genomes]
rs4960948	0.87[ASN][1000 genomes]
rs4960953	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4960954	0.95[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs4960959	0.87[CHB][hapmap];0.91[JPT][hapmap];0.90[LWK][hapmap];0.82[YRI][hapmap];0.89[ASN][1000 genomes]
rs4961044	0.83[CHB][hapmap]
rs4961045	0.83[CHB][hapmap]
rs4961068	0.91[CHB][hapmap]
rs4961071	0.87[ASN][1000 genomes]
rs4961072	0.81[ASN][1000 genomes]
rs4961074	1.00[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs4961075	0.81[ASN][1000 genomes]
rs4961077	0.83[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4961078	0.94[ASN][1000 genomes]
rs4961092	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57368948	0.86[ASN][1000 genomes]
rs57651622	0.87[ASN][1000 genomes]
rs57962008	0.87[ASN][1000 genomes]
rs58243820	0.87[ASN][1000 genomes]
rs59028033	0.87[ASN][1000 genomes]
rs60506092	0.94[ASN][1000 genomes]
rs61629815	0.87[ASN][1000 genomes]
rs62509924	0.86[ASN][1000 genomes]
rs62509930	0.87[ASN][1000 genomes]
rs62509933	0.85[ASN][1000 genomes]
rs6469703	0.83[ASN][1000 genomes]
rs6981194	0.92[ASN][1000 genomes]
rs6993377	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6999252	0.81[JPT][hapmap]
rs7000491	0.83[ASN][1000 genomes]
rs7001674	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7001699	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7005999	0.83[ASN][1000 genomes]
rs7016268	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7813508	1.00[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs7821560	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7830744	0.83[CHB][hapmap]
rs7831328	0.89[ASN][1000 genomes]
rs7836003	0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7837251	0.87[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs7846145	0.87[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs9643132	0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9643143	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9643144	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs975817	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428204	chr8:86405478-87312208	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv529563	chr8:86467090-87381984	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
3	nsv1028959	chr8:86835367-87142383	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv932023	chr8:86845979-87490694	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
5	nsv891147	chr8:86886950-87333968	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv1034721	chr8:86977250-87131151	Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	nsv891148	chr8:86987886-87149808	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv891149	chr8:87023306-87167184	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv1034855	chr8:87040075-87168730	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
10	nsv611673	chr8:87106710-87136320	Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	esv2761443	chr8:87109368-87170814	Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	nsv1020115	chr8:87111707-87167790	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv1026646	chr8:87111707-87177368	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4960955	OSGIN2	cis	parietal	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:87082400-87126200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr8:87115200-87121000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr8:87117600-87121600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr8:87119000-87121000	Enhancers	HepG2	liver
5	chr8:87119200-87122800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr8:87119600-87121400	Enhancers	Ovary	ovary
7	chr8:87120000-87121400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr8:87120000-87121600	Enhancers	Muscle Satellite Cultured Cells	--
9	chr8:87120000-87122000	Enhancers	A549	lung
10	chr8:87120000-87122200	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr8:87120000-87122200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr8:87120000-87122200	Enhancers	Hela-S3	cervix
13	chr8:87120000-87122200	Enhancers	NH-A	brain
14	chr8:87120000-87122200	Enhancers	Osteobl	bone
15	chr8:87120000-87122600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr8:87120000-87123200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr8:87120000-87123200	Enhancers	HMEC	breast
18	chr8:87120000-87123200	Enhancers	NHEK	skin
19	chr8:87120200-87120800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr8:87120200-87121000	Enhancers	Placenta Amnion	Placenta Amnion
21	chr8:87120200-87121000	Enhancers	Monocytes-CD14+_RO01746	blood
22	chr8:87120200-87121800	Weak transcription	Adipose Nuclei	Adipose
23	chr8:87120200-87121800	Enhancers	HSMMtube	muscle
24	chr8:87120200-87122200	Enhancers	Stomach Mucosa	stomach
25	chr8:87120400-87120800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
26	chr8:87120400-87121000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr8:87120400-87121000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr8:87120400-87121000	Enhancers	Sigmoid Colon	Sigmoid Colon
29	chr8:87120400-87121000	Enhancers	NHDF-Ad	bronchial
30	chr8:87120400-87121400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr8:87120400-87122200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr8:87120400-87122200	Enhancers	HUVEC	blood vessel
33	chr8:87120400-87122400	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr8:87120600-87120800	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chr8:87120600-87120800	Enhancers	Gastric	stomach
36	chr8:87120600-87121000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr8:87120600-87121000	Enhancers	Fetal Muscle Leg	muscle
38	chr8:87120600-87121000	Flanking Active TSS	HSMM	muscle
39	chr8:87120600-87121000	Enhancers	NHLF	lung
40	chr8:87120600-87121400	Enhancers	Rectal Mucosa Donor 31	rectum
41	chr8:87120600-87122000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr8:87120600-87122200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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