Variant report

Variant	rs41896
Chromosome Location	chr7:3826740-3826741
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:3824486..3827082-chr7:3833919..3835661,2	MCF-7	breast:

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1004142	1.00[AMR][1000 genomes]
rs10226577	1.00[AMR][1000 genomes]
rs10233941	1.00[CEU][hapmap];1.00[AMR][1000 genomes]
rs10257812	1.00[CEU][hapmap]
rs10260208	1.00[CEU][hapmap]
rs10264350	1.00[AMR][1000 genomes]
rs10277000	1.00[CEU][hapmap];1.00[AMR][1000 genomes]
rs10279770	1.00[AMR][1000 genomes]
rs10279868	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11978042	1.00[CEU][hapmap]
rs12113851	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs13437648	1.00[CEU][hapmap]
rs16870975	1.00[CEU][hapmap]
rs17133790	1.00[CEU][hapmap]
rs17133792	1.00[CEU][hapmap]
rs17133795	1.00[CEU][hapmap]
rs17133803	1.00[CEU][hapmap]
rs17133808	1.00[CEU][hapmap]
rs17133812	1.00[CEU][hapmap]
rs17134013	1.00[CEU][hapmap]
rs194370	1.00[CEU][hapmap];0.81[YRI][hapmap]
rs2014637	1.00[CEU][hapmap]
rs2214843	1.00[EUR][1000 genomes]
rs28379281	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28650199	1.00[AMR][1000 genomes]
rs28689669	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41881	1.00[CEU][hapmap]
rs41882	1.00[CEU][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes]
rs41883	1.00[CEU][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs41885	1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41887	0.89[YRI][hapmap];1.00[EUR][1000 genomes]
rs41888	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs41891	1.00[CEU][hapmap]
rs41894	1.00[CEU][hapmap]
rs41895	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs41897	0.86[YRI][hapmap];1.00[EUR][1000 genomes]
rs41898	1.00[CEU][hapmap];0.82[YRI][hapmap]
rs42233	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55806931	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56194378	1.00[EUR][1000 genomes]
rs6462287	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6462288	1.00[CEU][hapmap];0.96[YRI][hapmap];1.00[EUR][1000 genomes]
rs6949215	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs6951452	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6967027	1.00[CEU][hapmap];0.87[AMR][1000 genomes]
rs6970269	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6971516	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6975953	1.00[CEU][hapmap];0.89[YRI][hapmap]
rs73304253	0.87[AMR][1000 genomes]
rs73304284	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73306103	0.89[AMR][1000 genomes]
rs7791672	1.00[AMR][1000 genomes]
rs7793480	1.00[CEU][hapmap]
rs7805255	0.89[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018173	chr7:3258989-3879848	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv538660	chr7:3258989-3879848	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1016555	chr7:3298478-3872512	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv538661	chr7:3298478-3872512	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	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
6	nsv1021443	chr7:3705273-3889334	ZNF genes & repeats Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv1022650	chr7:3723035-3847680	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv1024704	chr7:3736254-3831859	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv1031610	chr7:3744536-3838844	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv1031999	chr7:3782751-3847680	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv538683	chr7:3782751-3847680	Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
12	esv2756505	chr7:3789992-3856544	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
13	nsv605937	chr7:3792038-3836379	Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
14	nsv605938	chr7:3792038-3852261	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
15	nsv1024292	chr7:3792949-3838578	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
16	nsv1027624	chr7:3808366-3923408	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
17	nsv538684	chr7:3808366-3923408	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:3825800-3827000	Enhancers	Fetal Brain Male	brain
2	chr7:3826400-3826800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:3826600-3828200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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