Variant report

Variant	rs6590857
Chromosome Location	chr11:101304409-101304410
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:100992008..101001878-chr11:101300412..101311512,29	MCF-7	breast:
2	chr11:101299708..101303554-chr11:101304150..101306716,3	MCF-7	breast:
3	chr11:101261268..101263471-chr11:101303237..101305024,2	MCF-7	breast:
4	chr11:101214168..101217557-chr11:101302222..101305735,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000082175	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10458946	0.90[AFR][1000 genomes]
rs11224752	0.91[AFR][1000 genomes]
rs11224753	0.90[AFR][1000 genomes]
rs11224754	0.90[AFR][1000 genomes]
rs11224755	0.90[AFR][1000 genomes]
rs11224756	0.90[AFR][1000 genomes]
rs11224758	0.90[AFR][1000 genomes]
rs11534488	0.84[AFR][1000 genomes]
rs11822280	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11824770	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12795350	0.82[AFR][1000 genomes]
rs12795968	0.90[AFR][1000 genomes]
rs12796333	0.90[AFR][1000 genomes]
rs12798288	0.90[AFR][1000 genomes]
rs12802904	0.90[AFR][1000 genomes]
rs12803560	0.90[AFR][1000 genomes]
rs12803803	0.91[AFR][1000 genomes]
rs12803811	0.90[AFR][1000 genomes]
rs17096639	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17096649	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1938991	0.91[AFR][1000 genomes]
rs1938994	0.80[GIH][hapmap]
rs2508355	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2508356	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2508361	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2508363	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2508364	1.00[EUR][1000 genomes]
rs2508370	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2508373	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2508376	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2513143	0.98[EUR][1000 genomes]
rs2513144	0.94[EUR][1000 genomes]
rs2513145	0.94[EUR][1000 genomes]
rs2513147	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2513148	0.98[EUR][1000 genomes]
rs2513171	1.00[EUR][1000 genomes]
rs2513173	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3016234	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3016235	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35452558	0.90[AFR][1000 genomes]
rs4754759	0.97[EUR][1000 genomes]
rs4754760	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55837513	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55997858	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56229466	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56284719	0.83[EUR][1000 genomes]
rs56334567	0.92[EUR][1000 genomes]
rs56380147	0.91[EUR][1000 genomes]
rs6590851	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6590852	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6590858	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7114691	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7115209	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7120480	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7125623	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72980031	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72980041	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72980076	0.95[EUR][1000 genomes]
rs72982215	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72982217	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72982219	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72982223	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72982226	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72982232	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72982238	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72982262	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72982273	0.89[AMR][1000 genomes]
rs744021	0.91[AFR][1000 genomes]
rs7926811	0.88[AFR][1000 genomes]
rs7928020	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7933788	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7935424	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7938675	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7938729	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7940538	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7949411	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv556131	chr11:100985777-101480017	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
2	nsv530644	chr11:101010088-101486038	Strong transcription Weak transcription Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
3	esv2753322	chr11:101052790-101311790	Flanking Bivalent TSS/Enh Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv898330	chr11:101243644-101722031	Enhancers Bivalent/Poised TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv468851	chr11:101268447-101330807	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv556132	chr11:101268447-101330807	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6590857	TMEM133	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:101300000-101307600	Enhancers	Fetal Lung	lung
2	chr11:101301200-101306200	Weak transcription	Stomach Smooth Muscle	stomach
3	chr11:101302000-101304800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr11:101302000-101304800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr11:101302000-101306400	Weak transcription	NHLF	lung
6	chr11:101302000-101316800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr11:101302200-101304800	Weak transcription	NHEK	skin
8	chr11:101302200-101306400	Weak transcription	Rectal Smooth Muscle	rectum
9	chr11:101302600-101307400	Enhancers	Colon Smooth Muscle	Colon
10	chr11:101303600-101305000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr11:101304000-101304800	Weak transcription	Fetal Brain Male	brain
12	chr11:101304000-101304800	Weak transcription	Ovary	ovary
13	chr11:101304000-101305200	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr11:101304000-101306400	Weak transcription	Fetal Stomach	stomach
15	chr11:101304200-101305400	Enhancers	HMEC	breast
16	chr11:101304400-101305000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr11:101304400-101312400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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