Variant report

Variant	rs16829724
Chromosome Location	chr3:119065581-119065582
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:119065560-119065768	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:119040293..119043055-chr3:119065307..119067902,3	MCF-7	breast:

Variant related genes	Relation type
RNU6-1127P	TF binding region
ENSG00000241155	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10511388	0.82[MEX][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12486197	1.00[CHB][hapmap]
rs16829700	0.81[EUR][1000 genomes]
rs16829712	0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs17281570	1.00[CEU][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs17281584	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17281591	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73854484	0.83[EUR][1000 genomes]
rs878808	0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs880097	0.83[EUR][1000 genomes]
rs9289128	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs935618	0.81[EUR][1000 genomes]
rs9835407	0.81[EUR][1000 genomes]
rs9845965	0.81[EUR][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	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	nsv829694	chr3:119011488-119153579	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119042800-119070600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr3:119042800-119072000	Weak transcription	Thymus	Thymus
3	chr3:119043000-119069000	Weak transcription	Primary T cells from cord blood	blood
4	chr3:119049200-119071200	Weak transcription	Aorta	Aorta
5	chr3:119049600-119068000	Weak transcription	NH-A	brain
6	chr3:119050800-119075800	Weak transcription	Pancreas	Pancrea
7	chr3:119053200-119087200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr3:119053400-119068200	Weak transcription	Right Ventricle	heart
9	chr3:119053400-119087000	Weak transcription	Fetal Muscle Trunk	muscle
10	chr3:119053600-119067800	Weak transcription	Fetal Lung	lung
11	chr3:119053600-119071400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr3:119056400-119067800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr3:119056400-119068200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr3:119056400-119071600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr3:119057800-119068000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr3:119060800-119067400	Weak transcription	Fetal Heart	heart
17	chr3:119063000-119070600	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr3:119063400-119068600	Weak transcription	GM12878-XiMat	blood
19	chr3:119063800-119068200	Weak transcription	Osteobl	bone
20	chr3:119064000-119066400	Enhancers	Lung	lung
21	chr3:119064000-119068200	Weak transcription	Brain Substantia Nigra	brain
22	chr3:119064200-119065800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:119064200-119065800	Enhancers	Fetal Muscle Leg	muscle
24	chr3:119064200-119066200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr3:119064200-119066200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr3:119064200-119066400	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr3:119064200-119066600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr3:119064400-119066200	Enhancers	Small Intestine	intestine
29	chr3:119064400-119073200	Enhancers	Adipose Nuclei	Adipose
30	chr3:119064600-119066000	Enhancers	Fetal Intestine Small	intestine
31	chr3:119064600-119066000	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr3:119064600-119066000	Enhancers	HSMMtube	muscle
33	chr3:119064600-119067800	Weak transcription	Brain Hippocampus Middle	brain
34	chr3:119064600-119068200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr3:119064800-119065600	Enhancers	HUES48 Cell Line	embryonic stem cell
36	chr3:119064800-119065600	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr3:119064800-119066000	Enhancers	HUES64 Cell Line	embryonic stem cell
38	chr3:119064800-119066200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr3:119064800-119066400	Weak transcription	Psoas Muscle	Psoas
40	chr3:119064800-119066800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr3:119064800-119067600	Enhancers	iPS-18 Cell Line	embryonic stem cell
42	chr3:119064800-119068200	Weak transcription	Placenta	Placenta
43	chr3:119064800-119071200	Weak transcription	Spleen	Spleen
44	chr3:119065000-119065600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr3:119065000-119065800	Weak transcription	Esophagus	oesophagus
46	chr3:119065000-119065800	Weak transcription	Right Atrium	heart
47	chr3:119065000-119066400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr3:119065000-119067600	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr3:119065000-119068200	Weak transcription	Ovary	ovary
50	chr3:119065000-119070400	Weak transcription	Sigmoid Colon	Sigmoid Colon

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