Variant report

Variant	rs10269554
Chromosome Location	chr7:3827541-3827542
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 148 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:131)

rs_ID	r²[population]
rs10226220	1.00[AMR][1000 genomes]
rs10227277	1.00[AMR][1000 genomes]
rs10230252	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10231172	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10232161	1.00[AMR][1000 genomes]
rs10232222	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10232460	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10232479	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10233053	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10235415	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10236208	1.00[AMR][1000 genomes]
rs10236726	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10237072	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10237207	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10237489	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10237769	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10238790	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10239119	1.00[AMR][1000 genomes]
rs10239349	1.00[AMR][1000 genomes]
rs10239755	1.00[AMR][1000 genomes]
rs10240271	1.00[AMR][1000 genomes]
rs10240744	0.91[AFR][1000 genomes]
rs10240764	1.00[AMR][1000 genomes]
rs10240770	1.00[AMR][1000 genomes]
rs10240776	1.00[AMR][1000 genomes]
rs10241150	1.00[YRI][hapmap]
rs10244131	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10244910	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs10246377	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10247342	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10248032	1.00[AMR][1000 genomes]
rs10249486	1.00[AMR][1000 genomes]
rs10249617	1.00[AMR][1000 genomes]
rs10250749	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10250969	1.00[AMR][1000 genomes]
rs10250990	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10251860	1.00[AMR][1000 genomes]
rs10252145	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10253717	1.00[AMR][1000 genomes]
rs10254515	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10254942	1.00[AMR][1000 genomes]
rs10255847	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs10256746	1.00[YRI][hapmap]
rs10259149	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10259421	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10259840	1.00[YRI][hapmap]
rs10259908	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10260110	1.00[YRI][hapmap]
rs10260973	1.00[AMR][1000 genomes]
rs10261101	1.00[AMR][1000 genomes]
rs10262755	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10262756	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10264034	1.00[AMR][1000 genomes]
rs10264365	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10265854	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs10266546	1.00[AMR][1000 genomes]
rs10269172	1.00[AMR][1000 genomes]
rs10269303	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs10269925	1.00[AMR][1000 genomes]
rs10270639	1.00[YRI][hapmap]
rs10271348	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10271361	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10271525	1.00[AMR][1000 genomes]
rs10274442	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10274450	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10275943	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10277140	1.00[AMR][1000 genomes]
rs10277615	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10277730	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10281035	1.00[AMR][1000 genomes]
rs10281383	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10282240	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10282727	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10479827	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs10479828	1.00[AMR][1000 genomes]
rs11505318	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11505319	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11505320	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11505321	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11505480	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11505481	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12333365	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12333373	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12333491	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12333534	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12333847	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12333850	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12333854	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16871049	1.00[AMR][1000 genomes]
rs28408018	1.00[AMR][1000 genomes]
rs28462157	1.00[AMR][1000 genomes]
rs28491068	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28496653	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28507850	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28532947	1.00[AMR][1000 genomes]
rs28541657	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28554772	1.00[AMR][1000 genomes]
rs28558397	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28560779	1.00[AMR][1000 genomes]
rs28563149	1.00[AMR][1000 genomes]
rs28568652	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28570515	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28578945	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28581916	1.00[AMR][1000 genomes]
rs28587155	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28593083	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28656287	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28656426	1.00[AMR][1000 genomes]
rs28692586	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28715920	1.00[AMR][1000 genomes]
rs28753192	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28765162	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28833830	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28839918	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28846162	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28856279	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28884793	1.00[AMR][1000 genomes]
rs34758548	1.00[AMR][1000 genomes]
rs57744825	1.00[AMR][1000 genomes]
rs58738480	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59292244	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59408720	1.00[AMR][1000 genomes]
rs60243310	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60409549	1.00[AMR][1000 genomes]
rs9655002	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9655324	1.00[YRI][hapmap]
rs9655326	1.00[YRI][hapmap]
rs9655328	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9655329	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9655341	1.00[AMR][1000 genomes]
rs9655342	1.00[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:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:3826600-3828200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr7:3826800-3827600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:3827000-3832400	Weak transcription	Fetal Brain Male	brain
4	chr7:3827000-3857200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr7:3827200-3827600	Enhancers	Adipose Nuclei	Adipose
6	chr7:3827200-3828000	Enhancers	Fetal Lung	lung
7	chr7:3827200-3828200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr7:3827400-3827600	Enhancers	Placenta	Placenta
9	chr7:3827400-3827800	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr7:3827400-3828000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr7:3827400-3828000	Enhancers	Esophagus	oesophagus
12	chr7:3827400-3828000	Active TSS	Fetal Kidney	kidney

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