Variant report

Variant	rs3777578
Chromosome Location	chr6:45908493-45908494
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	chr6:45908480..45910653-chr6:45930951..45933315,2	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12055836	1.00[CEU][hapmap];1.00[MEX][hapmap];0.89[AMR][1000 genomes]
rs12662995	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777566	1.00[CEU][hapmap];1.00[MEX][hapmap]
rs3777569	1.00[CEU][hapmap];0.89[AMR][1000 genomes]
rs3777570	1.00[CEU][hapmap];0.89[AMR][1000 genomes]
rs3777574	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777575	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777576	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.96[LWK][hapmap];0.98[MKK][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777577	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3798263	1.00[CEU][hapmap]
rs3798266	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs3822886	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3822887	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[JPT][hapmap];0.96[LWK][hapmap];0.98[MKK][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6907979	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9357496	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9395137	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs946226	1.00[CEU][hapmap];1.00[MEX][hapmap];0.89[AMR][1000 genomes]
rs949678	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.88[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532024	chr6:45475088-45982640	Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv517891	chr6:45899823-45915088	Genic enhancers Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45886800-45910600	Weak transcription	Psoas Muscle	Psoas
2	chr6:45895400-45910800	Weak transcription	Placenta	Placenta
3	chr6:45898600-45914600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr6:45898600-45916800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr6:45898800-45911000	Weak transcription	Adipose Nuclei	Adipose
6	chr6:45898800-45919200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr6:45899000-45910600	Weak transcription	Fetal Heart	heart
8	chr6:45899200-45910000	Strong transcription	Fetal Intestine Small	intestine
9	chr6:45903000-45917200	Strong transcription	Fetal Intestine Large	intestine
10	chr6:45903400-45914400	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr6:45905000-45911800	Strong transcription	Rectal Mucosa Donor 29	rectum
12	chr6:45905400-45908800	Weak transcription	Spleen	Spleen
13	chr6:45905400-45909600	Strong transcription	Skeletal Muscle Female	skeletal muscle
14	chr6:45906600-45909600	Strong transcription	Skeletal Muscle Male	skeletal muscle
15	chr6:45907000-45916600	Weak transcription	Pancreas	Pancrea
16	chr6:45907200-45910600	Strong transcription	Left Ventricle	heart
17	chr6:45907400-45917600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr6:45907800-45909600	Strong transcription	Right Ventricle	heart
19	chr6:45907800-45916400	Strong transcription	Rectal Mucosa Donor 31	rectum
20	chr6:45908000-45908800	Strong transcription	Duodenum Mucosa	Duodenum
21	chr6:45908000-45918600	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr6:45908200-45918200	Weak transcription	Colonic Mucosa	Colon
23	chr6:45908400-45910600	Weak transcription	Lung	lung

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