Variant report

Variant	rs31988
Chromosome Location	chr5:14797624-14797625
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: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1620976	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1679138	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs174018	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1812659	0.80[EUR][1000 genomes]
rs2448493	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2453320	0.95[ASN][1000 genomes]
rs258220	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs258232	0.95[ASN][1000 genomes]
rs25946	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs26304	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs26305	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs26306	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs27353	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs30613	0.93[ASN][1000 genomes]
rs30614	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs31907	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs31910	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs31911	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs31917	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs31931	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs31987	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs31989	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs31990	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs379016	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs39917	0.81[ASN][1000 genomes]
rs40402	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs412056	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs42274	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs43178	0.85[ASN][1000 genomes]
rs826351	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs826355	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs826356	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs826358	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[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:69 , 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	chr5:14790600-14797800	Weak transcription	HSMM	muscle
18	chr5:14790600-14809800	Weak transcription	Stomach Mucosa	stomach
19	chr5:14791000-14806000	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr5:14791000-14809600	Weak transcription	Primary hematopoietic stem cells	blood
21	chr5:14791400-14809800	Weak transcription	Aorta	Aorta
22	chr5:14791600-14802800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr5:14791600-14809600	Weak transcription	Fetal Intestine Large	intestine
24	chr5:14791600-14809600	Weak transcription	Small Intestine	intestine
25	chr5:14792200-14799400	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr5:14792400-14801800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr5:14793800-14801800	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr5:14793800-14802000	Weak transcription	Lung	lung
29	chr5:14793800-14804400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr5:14793800-14810000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr5:14794200-14798800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr5:14794400-14802000	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr5:14794400-14802200	Weak transcription	Right Ventricle	heart
34	chr5:14794400-14805800	Weak transcription	HepG2	liver
35	chr5:14794600-14806600	Weak transcription	Gastric	stomach
36	chr5:14795200-14798600	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr5:14795200-14801600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr5:14795200-14802000	Weak transcription	Left Ventricle	heart
39	chr5:14795200-14802000	Weak transcription	Thymus	Thymus
40	chr5:14795200-14809400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr5:14795200-14809400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr5:14795400-14797800	Weak transcription	Brain Substantia Nigra	brain
43	chr5:14795400-14800000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr5:14795400-14800600	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr5:14795400-14801600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr5:14795400-14802000	Weak transcription	Dnd41	blood
47	chr5:14795400-14805800	Weak transcription	Fetal Heart	heart
48	chr5:14795400-14809600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr5:14795400-14809600	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr5:14795600-14797800	Weak transcription	Brain Hippocampus Middle	brain

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