Variant report

Variant	rs258219
Chromosome Location	chr5:14791950-14791951
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:14789541..14791953-chr5:14870274..14872270,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000154122	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1061813	0.93[CHB][hapmap];0.88[ASN][1000 genomes]
rs11133799	0.88[ASN][1000 genomes]
rs1117282	0.81[ASN][1000 genomes]
rs12653321	0.88[ASN][1000 genomes]
rs13155894	0.86[ASN][1000 genomes]
rs1353258	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs1812658	0.81[ASN][1000 genomes]
rs2453316	0.87[ASN][1000 genomes]
rs258218	0.91[ASN][1000 genomes]
rs258222	0.93[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs258224	0.98[ASN][1000 genomes]
rs258225	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs258226	0.93[CHB][hapmap];0.86[YRI][hapmap];0.98[ASN][1000 genomes]
rs258227	0.93[CHB][hapmap];0.98[ASN][1000 genomes]
rs258228	0.98[ASN][1000 genomes]
rs258231	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs25957	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28005	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28006	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28108	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs30615	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs31909	1.00[CHB][hapmap];0.82[JPT][hapmap];0.96[ASN][1000 genomes]
rs31912	0.93[CHB][hapmap];0.91[ASN][1000 genomes]
rs31933	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs31990	0.87[CHB][hapmap]
rs33102	0.86[ASN][1000 genomes]
rs39636	0.86[ASN][1000 genomes]
rs39916	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs42679	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs573116	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs826352	0.93[CHB][hapmap];0.86[ASN][1000 genomes]
rs826357	0.82[ASN][1000 genomes]
rs879253	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs9790982	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

No data

Chromatin state (count:70 , 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	chr5:14777000-14794200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr5:14777200-14806200	Weak transcription	Stomach Smooth Muscle	stomach
6	chr5:14777200-14810400	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr5:14777200-14811400	Weak transcription	Colonic Mucosa	Colon
8	chr5:14778200-14805800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr5:14778200-14809400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr5:14778200-14817200	Weak transcription	Fetal Brain Female	brain
11	chr5:14780000-14794600	Weak transcription	Fetal Heart	heart
12	chr5:14781400-14796000	Weak transcription	Hela-S3	cervix
13	chr5:14781600-14794200	Weak transcription	Thymus	Thymus
14	chr5:14782200-14805800	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr5:14784600-14793400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr5:14784600-14793400	Weak transcription	Lung	lung
17	chr5:14784600-14793600	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr5:14784800-14797400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr5:14784800-14806600	Weak transcription	Adipose Nuclei	Adipose
20	chr5:14785000-14793400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr5:14785200-14793400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr5:14785200-14794000	Weak transcription	Gastric	stomach
23	chr5:14785600-14793400	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr5:14785800-14809600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr5:14787000-14794200	Weak transcription	Brain Anterior Caudate	brain
26	chr5:14788200-14793400	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr5:14788200-14793600	Weak transcription	Brain Hippocampus Middle	brain
28	chr5:14788400-14792200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr5:14788400-14809600	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr5:14788600-14792000	Weak transcription	Brain Substantia Nigra	brain
31	chr5:14788600-14792000	Weak transcription	Right Ventricle	heart
32	chr5:14788600-14793400	Weak transcription	Brain Angular Gyrus	brain
33	chr5:14788600-14793400	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr5:14788600-14809600	Weak transcription	Psoas Muscle	Psoas
35	chr5:14788800-14793600	Weak transcription	Brain Cingulate Gyrus	brain
36	chr5:14788800-14802000	Weak transcription	Spleen	Spleen
37	chr5:14788800-14809600	Weak transcription	Liver	Liver
38	chr5:14789000-14793400	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr5:14789400-14792000	Enhancers	Primary T cells from cord blood	blood
40	chr5:14789400-14792200	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr5:14789800-14792200	Enhancers	Primary T cells fromperipheralblood	blood
42	chr5:14789800-14792800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
43	chr5:14790200-14792000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr5:14790200-14792200	Enhancers	Primary T killer memory cells from peripheral blood	blood
45	chr5:14790200-14792400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr5:14790200-14792400	Enhancers	Dnd41	blood
47	chr5:14790200-14792600	Enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr5:14790600-14793600	Weak transcription	HepG2	liver
49	chr5:14790600-14797800	Weak transcription	HSMM	muscle
50	chr5:14790600-14809800	Weak transcription	Stomach Mucosa	stomach

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