Variant report

Variant	rs258220
Chromosome Location	chr5:14799695-14799696
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	chr5:14796002..14798417-chr5:14798624..14800724,2	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1620976	0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1679138	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs174018	0.81[ASN][1000 genomes]
rs1812659	0.82[EUR][1000 genomes]
rs2448493	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2453320	0.93[ASN][1000 genomes]
rs258232	0.93[ASN][1000 genomes]
rs25946	0.83[CHB][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs26304	0.86[CEU][hapmap];0.94[CHB][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs26305	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs26306	0.89[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs27353	0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs30613	0.94[CHB][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs31907	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs31910	0.96[CEU][hapmap];0.94[CHB][hapmap];0.86[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs31911	0.93[CEU][hapmap];0.87[CHB][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs31917	0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs31931	0.81[ASN][1000 genomes]
rs31987	0.96[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs31988	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs31989	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs31990	0.80[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs379016	0.89[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs40402	0.86[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs412056	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs42274	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs43178	0.82[ASN][1000 genomes]
rs826351	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs826355	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs826356	0.89[CEU][hapmap];0.88[CHB][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs826358	0.83[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018187	chr5:14385164-15127103	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv948447	chr5:14771247-14852610	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	3 gene(s)	inside rSNPs	diseases
3	nsv830212	chr5:14784197-14966683	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
4	nsv968141	chr5:14796725-14801342	Weak transcription Enhancers Genic enhancers Strong transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:14753600-14801600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr5:14767400-14809800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr5:14776800-14809400	Weak transcription	HMEC	breast
4	chr5:14777200-14806200	Weak transcription	Stomach Smooth Muscle	stomach
5	chr5:14777200-14810400	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr5:14777200-14811400	Weak transcription	Colonic Mucosa	Colon
7	chr5:14778200-14805800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr5:14778200-14809400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr5:14778200-14817200	Weak transcription	Fetal Brain Female	brain
10	chr5:14782200-14805800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr5:14784800-14806600	Weak transcription	Adipose Nuclei	Adipose
12	chr5:14785800-14809600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr5:14788400-14809600	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr5:14788600-14809600	Weak transcription	Psoas Muscle	Psoas
15	chr5:14788800-14802000	Weak transcription	Spleen	Spleen
16	chr5:14788800-14809600	Weak transcription	Liver	Liver
17	chr5:14790600-14809800	Weak transcription	Stomach Mucosa	stomach
18	chr5:14791000-14806000	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr5:14791000-14809600	Weak transcription	Primary hematopoietic stem cells	blood
20	chr5:14791400-14809800	Weak transcription	Aorta	Aorta
21	chr5:14791600-14802800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr5:14791600-14809600	Weak transcription	Fetal Intestine Large	intestine
23	chr5:14791600-14809600	Weak transcription	Small Intestine	intestine
24	chr5:14792400-14801800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr5:14793800-14801800	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr5:14793800-14802000	Weak transcription	Lung	lung
27	chr5:14793800-14804400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr5:14793800-14810000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr5:14794400-14802000	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr5:14794400-14802200	Weak transcription	Right Ventricle	heart
31	chr5:14794400-14805800	Weak transcription	HepG2	liver
32	chr5:14794600-14806600	Weak transcription	Gastric	stomach
33	chr5:14795200-14801600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr5:14795200-14802000	Weak transcription	Left Ventricle	heart
35	chr5:14795200-14802000	Weak transcription	Thymus	Thymus
36	chr5:14795200-14809400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr5:14795200-14809400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr5:14795400-14800000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr5:14795400-14800600	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr5:14795400-14801600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr5:14795400-14802000	Weak transcription	Dnd41	blood
42	chr5:14795400-14805800	Weak transcription	Fetal Heart	heart
43	chr5:14795400-14809600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr5:14795400-14809600	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr5:14795600-14809600	Weak transcription	Brain Anterior Caudate	brain
46	chr5:14795800-14800400	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr5:14795800-14801800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr5:14795800-14804400	Weak transcription	Duodenum Mucosa	Duodenum
49	chr5:14796000-14802600	Weak transcription	Fetal Intestine Small	intestine
50	chr5:14796400-14804600	Weak transcription	Hela-S3	cervix

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