Variant report

Variant	rs16829477
Chromosome Location	chr3:118926172-118926173
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:118925125..118927073-chr3:118927779..118929469,2	MCF-7	breast:
2	chr3:118924439..118927161-chr3:118936255..118939127,2	MCF-7	breast:
3	chr3:118925359..118927166-chr3:118958232..118960425,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000121578	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10511382	0.82[CHB][hapmap];0.82[JPT][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11927939	0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12634868	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13081519	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes]
rs16829479	1.00[CHB][hapmap];0.82[JPT][hapmap];0.93[ASN][1000 genomes]
rs3796356	0.96[EUR][1000 genomes]
rs3796357	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes]
rs4370022	0.82[CHB][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4687840	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4687980	1.00[CHB][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4687981	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4687982	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57258193	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs58939003	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61162364	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6438502	1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[EUR][1000 genomes]
rs6438506	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs7426444	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes]
rs9840317	0.87[EUR][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	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	esv18354	chr3:118855337-119000251	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv591362	chr3:118906442-118948155	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:118904600-118936400	Weak transcription	Gastric	stomach
2	chr3:118908400-118928200	Weak transcription	Fetal Stomach	stomach
3	chr3:118911800-118932600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:118915200-118928400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:118915200-118934800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr3:118920400-118930400	Weak transcription	Fetal Kidney	kidney
7	chr3:118921000-118928000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr3:118921400-118931200	Weak transcription	Brain Cingulate Gyrus	brain
9	chr3:118922200-118927400	Weak transcription	HSMM	muscle
10	chr3:118922600-118929000	Weak transcription	Spleen	Spleen
11	chr3:118922800-118926200	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr3:118922800-118926200	Enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr3:118923000-118927600	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr3:118923000-118929000	Weak transcription	Brain Germinal Matrix	brain
15	chr3:118923200-118927400	Weak transcription	Stomach Smooth Muscle	stomach
16	chr3:118923400-118926800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr3:118923400-118927000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr3:118923400-118927400	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr3:118923600-118930800	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr3:118923800-118931600	Enhancers	Stomach Mucosa	stomach
21	chr3:118924200-118926600	Enhancers	Right Atrium	heart
22	chr3:118924200-118926800	Enhancers	Primary T cells fromperipheralblood	blood
23	chr3:118924200-118927200	Enhancers	Fetal Thymus	thymus
24	chr3:118924200-118927800	Weak transcription	Fetal Muscle Trunk	muscle
25	chr3:118924200-118931600	Weak transcription	NHDF-Ad	bronchial
26	chr3:118924400-118926600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr3:118924400-118927600	Weak transcription	Aorta	Aorta
28	chr3:118924400-118928200	Enhancers	Primary neutrophils fromperipheralblood	blood
29	chr3:118924400-118929200	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr3:118924400-118929800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr3:118924400-118933200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr3:118924400-118959000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr3:118924600-118926400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr3:118924600-118926400	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr3:118924600-118926800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr3:118924600-118927200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr3:118924600-118927800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr3:118924600-118928000	Weak transcription	Ovary	ovary
39	chr3:118924600-118929000	Weak transcription	Colonic Mucosa	Colon
40	chr3:118924600-118930000	Weak transcription	Osteobl	bone
41	chr3:118924600-118930200	Weak transcription	Fetal Lung	lung
42	chr3:118924600-118945600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr3:118924800-118926200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr3:118924800-118927200	Enhancers	NHEK	skin
45	chr3:118924800-118927400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr3:118924800-118928000	Weak transcription	Fetal Muscle Leg	muscle
47	chr3:118924800-118928400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr3:118924800-118929400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr3:118924800-118931200	Weak transcription	Right Ventricle	heart
50	chr3:118925000-118926800	Enhancers	HMEC	breast

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