Variant report

Variant	rs16829712
Chromosome Location	chr3:119059368-119059369
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	chr3:119039655..119042714-chr3:119058706..119061390,3	MCF-7	breast:
2	chr3:119057410..119059472-chr3:119060813..119062676,2	K562	blood:

Variant related genes	Relation type
ENSG00000241155	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10511388	1.00[CEU][hapmap];1.00[CHD][hapmap];0.86[TSI][hapmap];0.94[EUR][1000 genomes]
rs16829700	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs16829724	0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs17203055	1.00[CHD][hapmap]
rs17281570	0.86[TSI][hapmap]
rs17281584	0.94[EUR][1000 genomes]
rs17281591	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs4687849	1.00[CHB][hapmap]
rs4687850	1.00[CHB][hapmap]
rs4687999	1.00[CHB][hapmap]
rs4688000	1.00[CHB][hapmap]
rs7614346	1.00[CHD][hapmap]
rs878808	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs880097	0.94[EUR][1000 genomes]
rs9289128	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935618	0.92[EUR][1000 genomes]
rs9832224	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9835407	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9845965	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.92[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:50 , 50 per page) page: 1

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	chr3:119043200-119062400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr3:119046000-119064200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr3:119046000-119064600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr3:119048800-119062800	Weak transcription	Osteobl	bone
8	chr3:119049200-119062200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr3:119049200-119071200	Weak transcription	Aorta	Aorta
10	chr3:119049600-119068000	Weak transcription	NH-A	brain
11	chr3:119050000-119062000	Weak transcription	Placenta	Placenta
12	chr3:119050800-119064600	Weak transcription	HSMMtube	muscle
13	chr3:119050800-119075800	Weak transcription	Pancreas	Pancrea
14	chr3:119051000-119064800	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr3:119052000-119059400	Weak transcription	HUVEC	blood vessel
16	chr3:119052000-119062000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr3:119052000-119064600	Weak transcription	Fetal Intestine Small	intestine
18	chr3:119052600-119064200	Weak transcription	Brain Cingulate Gyrus	brain
19	chr3:119053200-119064800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr3:119053200-119087200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr3:119053400-119064400	Weak transcription	Psoas Muscle	Psoas
22	chr3:119053400-119064400	Weak transcription	Spleen	Spleen
23	chr3:119053400-119068200	Weak transcription	Right Ventricle	heart
24	chr3:119053400-119087000	Weak transcription	Fetal Muscle Trunk	muscle
25	chr3:119053600-119064200	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr3:119053600-119067800	Weak transcription	Fetal Lung	lung
27	chr3:119053600-119071400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr3:119053800-119059600	Weak transcription	Adipose Nuclei	Adipose
29	chr3:119054600-119059400	Weak transcription	Lung	lung
30	chr3:119054600-119062400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr3:119056200-119062200	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr3:119056400-119061600	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr3:119056400-119064200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr3:119056400-119067800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr3:119056400-119068200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr3:119056400-119071600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr3:119056600-119062200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr3:119056600-119064400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr3:119057000-119064800	Weak transcription	HSMM	muscle
40	chr3:119057800-119060400	Enhancers	Cortex derived primary cultured neurospheres	brain
41	chr3:119057800-119068000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr3:119058000-119064200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:119058200-119060800	Weak transcription	NHDF-Ad	bronchial
44	chr3:119058200-119064400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr3:119058400-119059400	Enhancers	GM12878-XiMat	blood
46	chr3:119059000-119059600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr3:119059000-119060800	Enhancers	Fetal Heart	heart
48	chr3:119059200-119059400	Enhancers	Left Ventricle	heart
49	chr3:119059200-119059600	Enhancers	Fetal Stomach	stomach
50	chr3:119059200-119060200	Enhancers	Ovary	ovary

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