Variant report

Variant	rs628980
Chromosome Location	chr6:11497336-11497337
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:11172752..11173484-chr6:11496207..11497499,6	MCF-7	breast:
2	chr6:11143734..11145501-chr6:11496107..11497580,26	MCF-7	breast:
3	chr6:11144071..11145293-chr6:11495634..11497487,8	K562	blood:
4	chr6:11356223..11359281-chr6:11494815..11498233,5	MCF-7	breast:
5	chr6:11230707..11237186-chr6:11493072..11498269,11	MCF-7	breast:
6	chr6:11143454..11145339-chr6:11495146..11498003,3	MCF-7	breast:
7	chr6:11142754..11146580-chr6:11494452..11498982,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111859	Chromatin interaction

Extended variants
information (count: 113 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs11751931	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16871371	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17607537	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17607558	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17675742	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17675772	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2140109	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2177158	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2177159	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2327440	0.84[JPT][hapmap]
rs34066851	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34255222	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34336996	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34342746	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34363244	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34486680	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34586980	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34630993	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34678413	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34793558	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34951511	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35074878	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35087778	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35100959	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35160576	0.84[EUR][1000 genomes]
rs35250180	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35491413	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35658210	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35877256	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35938392	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs36021289	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs36023953	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs36053861	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs36120363	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3942485	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4711303	0.94[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4713556	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4713562	0.94[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4713569	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4713577	0.93[CEU][hapmap];1.00[JPT][hapmap]
rs4713579	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs471560	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs471752	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs478147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs483637	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs490327	0.80[EUR][1000 genomes]
rs490466	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs509971	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs513870	0.80[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.88[MEX][hapmap];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs519140	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs524159	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs528679	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs538808	0.95[ASN][1000 genomes]
rs539160	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs552681	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs554671	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs555034	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs555742	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56055084	0.86[ASN][1000 genomes]
rs566237	0.80[CEU][hapmap];0.84[JPT][hapmap];0.84[AMR][1000 genomes]
rs571683	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs573082	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs574254	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs578507	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs581285	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs586105	0.82[ASN][1000 genomes]
rs598907	1.00[CEU][hapmap];0.94[CHB][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs605058	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs606402	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap]
rs620729	0.80[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.88[MEX][hapmap]
rs62394918	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62394920	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62394921	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62394922	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62394923	0.80[EUR][1000 genomes]
rs62394924	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62394925	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62394926	0.85[EUR][1000 genomes]
rs62394927	0.85[EUR][1000 genomes]
rs62394928	0.85[EUR][1000 genomes]
rs637564	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6457608	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs661055	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs663283	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66502560	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67452935	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs675565	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67807015	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs678862	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs685384	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs687163	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6904209	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6907890	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6907900	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6907944	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6922323	0.84[EUR][1000 genomes]
rs6923613	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6923798	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6936326	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs7752671	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs821443	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9348893	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9357151	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9366802	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9368729	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9380321	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9394108	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9394109	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9394115	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9394119	0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021078	chr6:10819083-11558560	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv538135	chr6:10819083-11558560	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv432848	chr6:11371614-11560114	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs628980	TMEM170B	cis	Adipose Subcutaneous	GTEx
rs628980	GCNT2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:11492000-11498200	Enhancers	A549	lung
2	chr6:11492200-11497400	Enhancers	HepG2	liver
3	chr6:11493000-11499800	Weak transcription	NH-A	brain
4	chr6:11493400-11497600	Enhancers	Placenta Amnion	Placenta Amnion
5	chr6:11493400-11498200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr6:11494200-11498200	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr6:11494400-11500600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr6:11496400-11497800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr6:11496400-11498600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
10	chr6:11496600-11497600	Enhancers	Primary hematopoietic stem cells	blood
11	chr6:11496600-11497600	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr6:11496600-11499800	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr6:11496600-11500000	Weak transcription	Osteobl	bone
14	chr6:11496600-11500200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:11496800-11497400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr6:11496800-11497400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr6:11496800-11497400	Flanking Active TSS	GM12878-XiMat	blood
18	chr6:11497000-11497800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
19	chr6:11497000-11498000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr6:11497000-11498000	Weak transcription	HMEC	breast
21	chr6:11497000-11498400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr6:11497000-11499800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr6:11497000-11500000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr6:11497000-11500200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr6:11497200-11497600	Enhancers	Primary neutrophils fromperipheralblood	blood
26	chr6:11497200-11498200	Weak transcription	Placenta	Placenta
27	chr6:11497200-11499200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr6:11497200-11500000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr6:11497200-11500000	Weak transcription	NHEK	skin

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