Variant report

Variant	rs6798309
Chromosome Location	chr3:53024022-53024023
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 91 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs34397833	1.00[AMR][1000 genomes]
rs35981653	1.00[AMR][1000 genomes]
rs56665986	0.97[AFR][1000 genomes]
rs56835905	0.91[AFR][1000 genomes]
rs56895623	0.98[AFR][1000 genomes]
rs57273027	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57465047	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57561909	0.90[AFR][1000 genomes]
rs57640885	1.00[AMR][1000 genomes]
rs57654423	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58249114	0.98[AFR][1000 genomes]
rs58888768	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59224641	0.97[AFR][1000 genomes]
rs59838592	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60207422	1.00[AMR][1000 genomes]
rs60648378	0.97[AFR][1000 genomes]
rs60805548	1.00[AMR][1000 genomes]
rs61324750	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61331336	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61437303	0.91[AFR][1000 genomes]
rs61438885	0.91[AFR][1000 genomes]
rs6776862	1.00[AMR][1000 genomes]
rs6787566	0.94[YRI][hapmap]
rs6798669	0.98[AFR][1000 genomes]
rs72954390	1.00[AMR][1000 genomes]
rs72954402	1.00[AMR][1000 genomes]
rs72959475	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72959477	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72959478	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72959479	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72959482	0.86[AFR][1000 genomes]
rs72959487	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72959494	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72959499	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72961704	0.86[AFR][1000 genomes]
rs72961705	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72961708	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72961711	1.00[AMR][1000 genomes]
rs72961724	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72961730	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72961733	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72961742	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72961752	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72965340	0.98[AFR][1000 genomes]
rs72965348	0.98[AFR][1000 genomes]
rs72965358	0.95[AFR][1000 genomes]
rs72965359	0.98[AFR][1000 genomes]
rs72965366	0.91[AFR][1000 genomes]
rs72965370	0.93[AFR][1000 genomes]
rs72965381	0.92[AFR][1000 genomes]
rs7618417	0.95[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:40 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3446915	chr3:52786850-53049217	Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	esv1818974	chr3:52966316-53096394	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv3823	chr3:53003659-53051063	Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	esv2756989	chr3:53006055-53039455	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	esv2759149	chr3:53006055-53039455	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv1001449	chr3:53009379-53039104	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv998180	chr3:53011207-53039267	Weak transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	esv1802390	chr3:53011741-53039205	Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv1008590	chr3:53011741-53039267	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv1002814	chr3:53011741-53039665	Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv1011757	chr3:53012195-53039104	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv1011874	chr3:53019183-53039104	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv1003328	chr3:53019183-53039665	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	nsv1006561	chr3:53019313-53039104	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	nsv1002983	chr3:53021057-53039104	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	nsv1003421	chr3:53021057-53039205	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
17	nsv1004368	chr3:53021057-53039665	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
18	nsv1000407	chr3:53022010-53033136	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
19	nsv1004160	chr3:53022010-53039104	Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
20	nsv1004730	chr3:53022010-53039267	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
21	nsv1014506	chr3:53022010-53039665	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
22	nsv1003254	chr3:53022855-53038890	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
23	nsv1003591	chr3:53022855-53039104	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
24	nsv1010511	chr3:53022855-53039477	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
25	nsv999427	chr3:53022855-53041873	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
26	nsv1007659	chr3:53022881-53039104	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
27	nsv1014099	chr3:53022912-53039104	Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
28	nsv1011388	chr3:53022912-53039665	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
29	nsv1014633	chr3:53022937-53034528	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
30	nsv1007315	chr3:53022937-53037242	Enhancers Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
31	nsv1013928	chr3:53022937-53038932	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
32	nsv1009671	chr3:53022937-53039104	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
33	nsv1013733	chr3:53022937-53039205	Strong transcription Active TSS Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
34	nsv1002820	chr3:53022937-53039477	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
35	nsv1012396	chr3:53023199-53037242	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
36	nsv1003018	chr3:53023199-53039104	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
37	nsv1013774	chr3:53023199-53039267	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
38	nsv1004325	chr3:53023199-53039665	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
39	esv2763768	chr3:53023211-53045925	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
40	esv1796300	chr3:53024022-53038983	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52965000-53039800	Weak transcription	Left Ventricle	heart
2	chr3:53008400-53031000	Weak transcription	Hela-S3	cervix
3	chr3:53012600-53032600	Weak transcription	Pancreas	Pancrea
4	chr3:53016200-53029400	Weak transcription	Fetal Intestine Small	intestine
5	chr3:53018000-53030400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr3:53018000-53044200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr3:53018200-53045200	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr3:53018600-53032800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr3:53019000-53057200	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr3:53019200-53032800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr3:53019200-53039600	Weak transcription	GM12878-XiMat	blood
12	chr3:53019600-53056400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr3:53019800-53024200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr3:53019800-53024200	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr3:53019800-53024400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr3:53019800-53044400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr3:53020400-53024200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr3:53020400-53024400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr3:53020600-53057000	Weak transcription	Dnd41	blood
20	chr3:53022600-53030600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr3:53022600-53043000	Weak transcription	Primary B cells from peripheral blood	blood
22	chr3:53022600-53050400	Weak transcription	Primary B cells from cord blood	blood
23	chr3:53023000-53025400	Weak transcription	Lung	lung
24	chr3:53023400-53024400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr3:53023400-53026200	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr3:53023800-53025200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr3:53024000-53024200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
28	chr3:53024000-53025000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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