Variant report

Variant	rs6962750
Chromosome Location	chr7:3948683-3948684
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:3947932..3950368-chr7:3952794..3955461,2	MCF-7	breast:

Extended variants
information (count: 118 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs1013880	0.97[ASN][1000 genomes]
rs10215004	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10215340	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10228397	0.87[ASN][1000 genomes]
rs10241703	0.85[ASN][1000 genomes]
rs10242459	0.85[ASN][1000 genomes]
rs10243770	0.85[ASN][1000 genomes]
rs10244636	0.85[ASN][1000 genomes]
rs10245389	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10249255	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10250659	0.88[ASN][1000 genomes]
rs10254099	0.85[ASN][1000 genomes]
rs10262942	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10263496	0.84[ASN][1000 genomes]
rs10267786	0.90[ASN][1000 genomes]
rs10273444	0.87[ASN][1000 genomes]
rs10485864	0.87[ASN][1000 genomes]
rs10951368	0.98[ASN][1000 genomes]
rs10951374	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11514766	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11971293	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11973090	0.85[ASN][1000 genomes]
rs11973380	0.97[ASN][1000 genomes]
rs11974190	0.82[ASN][1000 genomes]
rs11974357	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11980947	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11982345	0.89[ASN][1000 genomes]
rs11983563	0.97[ASN][1000 genomes]
rs12531046	0.90[ASN][1000 genomes]
rs12532171	0.98[ASN][1000 genomes]
rs12533946	0.97[ASN][1000 genomes]
rs12690803	0.85[ASN][1000 genomes]
rs12690804	0.85[ASN][1000 genomes]
rs12701262	0.90[ASN][1000 genomes]
rs12701271	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12701272	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13245096	0.97[ASN][1000 genomes]
rs1476644	0.83[ASN][1000 genomes]
rs17261199	0.84[ASN][1000 genomes]
rs1962784	0.85[ASN][1000 genomes]
rs1962785	0.85[ASN][1000 genomes]
rs2007554	0.85[ASN][1000 genomes]
rs2057919	0.85[ASN][1000 genomes]
rs2057920	0.85[ASN][1000 genomes]
rs2057921	0.85[ASN][1000 genomes]
rs2079376	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2079377	0.85[ASN][1000 genomes]
rs2079378	0.82[ASN][1000 genomes]
rs2097899	0.82[ASN][1000 genomes]
rs28491320	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2880159	0.97[ASN][1000 genomes]
rs28845270	0.85[ASN][1000 genomes]
rs34730154	0.87[ASN][1000 genomes]
rs4431501	0.85[ASN][1000 genomes]
rs6462407	0.85[ASN][1000 genomes]
rs6462411	0.85[ASN][1000 genomes]
rs6462412	0.85[ASN][1000 genomes]
rs6462413	0.85[ASN][1000 genomes]
rs6462423	0.87[ASN][1000 genomes]
rs6462447	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6944393	0.87[ASN][1000 genomes]
rs6952864	0.85[ASN][1000 genomes]
rs6953282	0.85[ASN][1000 genomes]
rs6953707	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6954370	0.85[ASN][1000 genomes]
rs6955650	0.82[ASN][1000 genomes]
rs6956020	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6956479	0.85[ASN][1000 genomes]
rs6958385	0.85[ASN][1000 genomes]
rs6958535	0.85[ASN][1000 genomes]
rs6959492	0.92[ASN][1000 genomes]
rs6959674	0.97[ASN][1000 genomes]
rs6961561	0.85[ASN][1000 genomes]
rs6962058	0.93[ASN][1000 genomes]
rs6962389	0.93[ASN][1000 genomes]
rs6963058	0.85[ASN][1000 genomes]
rs6963674	0.85[ASN][1000 genomes]
rs6968148	0.85[ASN][1000 genomes]
rs6968267	0.85[ASN][1000 genomes]
rs6968272	0.85[ASN][1000 genomes]
rs6968444	0.85[ASN][1000 genomes]
rs6968948	0.85[ASN][1000 genomes]
rs6970116	0.85[ASN][1000 genomes]
rs6971639	0.85[ASN][1000 genomes]
rs6971803	0.85[ASN][1000 genomes]
rs6971828	0.83[ASN][1000 genomes]
rs6971873	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6971953	0.85[ASN][1000 genomes]
rs6972806	0.85[ASN][1000 genomes]
rs6975723	0.80[ASN][1000 genomes]
rs6977305	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6977844	0.85[ASN][1000 genomes]
rs6978060	0.85[ASN][1000 genomes]
rs6978318	0.85[ASN][1000 genomes]
rs7783415	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7786556	0.92[ASN][1000 genomes]
rs7800775	0.89[ASN][1000 genomes]
rs7804166	0.90[ASN][1000 genomes]
rs7809616	0.89[ASN][1000 genomes]
rs874344	0.97[ASN][1000 genomes]
rs917168	0.87[ASN][1000 genomes]
rs9655007	0.82[ASN][1000 genomes]
rs9655343	0.85[ASN][1000 genomes]
rs9655347	0.87[ASN][1000 genomes]
rs9655348	0.87[ASN][1000 genomes]
rs9886069	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9886234	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9986911	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021650	chr7:3665232-4577439	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1029406	chr7:3860894-4477095	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv538685	chr7:3860894-4477095	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1026410	chr7:3869104-4383606	Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1025497	chr7:3905444-4176032	Enhancers Strong transcription ZNF genes & repeats Genic enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv538686	chr7:3905444-4176032	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv433014	chr7:3910039-4054769	Strong transcription Enhancers Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv518377	chr7:3939055-3978342	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv1030082	chr7:3941203-3986403	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv1020222	chr7:3946655-3985756	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:3901200-3959600	Weak transcription	Pancreas	Pancrea
2	chr7:3906800-3949000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr7:3936800-3974200	Weak transcription	Aorta	Aorta
4	chr7:3940600-3953800	Weak transcription	Fetal Brain Male	brain
5	chr7:3946400-3948800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr7:3947200-3951600	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr7:3947800-3949800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr7:3948000-3949000	Weak transcription	Brain Hippocampus Middle	brain
9	chr7:3948000-3949200	Enhancers	Fetal Muscle Trunk	muscle
10	chr7:3948000-3950600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr7:3948200-3949000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr7:3948200-3951400	Weak transcription	Fetal Lung	lung
13	chr7:3948200-3955000	Weak transcription	Spleen	Spleen
14	chr7:3948600-3950000	Enhancers	Brain Substantia Nigra	brain

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