Variant report

Variant	rs246142
Chromosome Location	chr16:69459477-69459478
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:69457747..69460846-chr16:69598845..69601292,3	MCF-7	breast:
2	chr16:69457237..69459987-chr16:69598210..69601258,3	K562	blood:
3	chr16:69456628..69460851-chr16:69598482..69601931,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000223109	Chromatin interaction
ENSG00000102908	Chromatin interaction

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

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

rs_ID	r²[population]
rs10048086	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11075720	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs153053	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs153058	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs246132	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs246138	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs246140	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs246143	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs246144	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs246145	0.84[CEU][hapmap];0.83[JPT][hapmap]
rs246148	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3743670	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4783708	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6499227	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7185800	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7206737	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs728546	0.85[CEU][hapmap];0.83[JPT][hapmap]
rs8064195	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs862349	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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	nsv1064808	chr16:69271190-69552951	Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv542940	chr16:69271190-69552951	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	nsv431514	chr16:69428599-69581699	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:69456800-69460000	Active TSS	GM12878-XiMat	blood
2	chr16:69457000-69459600	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr16:69457200-69459600	Active TSS	Brain Anterior Caudate	brain
4	chr16:69457400-69459600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr16:69457400-69459800	Active TSS	Breast Myoepithelial Primary Cells	Breast
6	chr16:69457400-69459800	Active TSS	NHDF-Ad	bronchial
7	chr16:69457600-69459600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr16:69457600-69459800	Active TSS	Brain Cingulate Gyrus	brain
9	chr16:69457600-69459800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr16:69457800-69459600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr16:69457800-69459600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr16:69457800-69459600	Active TSS	Fetal Intestine Small	intestine
13	chr16:69457800-69459600	Active TSS	Stomach Smooth Muscle	stomach
14	chr16:69457800-69459600	Active TSS	HSMM	muscle
15	chr16:69457800-69459800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr16:69457800-69459800	Active TSS	iPS-15b Cell Line	embryonic stem cell
17	chr16:69457800-69459800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr16:69457800-69459800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr16:69457800-69460000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr16:69458000-69459600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
21	chr16:69458000-69459600	Active TSS	H1 Cell Line	embryonic stem cell
22	chr16:69458000-69459600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr16:69458000-69459600	Active TSS	Fetal Intestine Large	intestine
24	chr16:69458000-69459800	Active TSS	ES-I3 Cell Line	embryonic stem cell
25	chr16:69458000-69459800	Active TSS	H9 Cell Line	embryonic stem cell
26	chr16:69458000-69459800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr16:69458000-69459800	Active TSS	HUES48 Cell Line	embryonic stem cell
28	chr16:69458000-69459800	Active TSS	HUES6 Cell Line	embryonic stem cell
29	chr16:69458000-69459800	Active TSS	iPS-18 Cell Line	embryonic stem cell
30	chr16:69458000-69459800	Active TSS	NHLF	lung
31	chr16:69458000-69460000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr16:69458000-69460200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr16:69458000-69460200	Active TSS	HMEC	breast
34	chr16:69458200-69459600	Active TSS	Rectal Mucosa Donor 31	rectum
35	chr16:69458200-69459600	Active TSS	HSMMtube	muscle
36	chr16:69458200-69459800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr16:69458200-69460600	Active TSS	A549	lung
38	chr16:69458200-69460600	Active TSS	Hela-S3	cervix
39	chr16:69458400-69459600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr16:69458400-69459600	Active TSS	Fetal Thymus	thymus
41	chr16:69458400-69459600	Active TSS	NH-A	brain
42	chr16:69458400-69460800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
43	chr16:69458600-69459600	Bivalent/Poised TSS	HepG2	liver
44	chr16:69458600-69459800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
45	chr16:69458600-69460200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr16:69458800-69459600	Flanking Active TSS	Primary T cells from cord blood	blood
47	chr16:69458800-69459600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
48	chr16:69458800-69459800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr16:69458800-69459800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr16:69458800-69459800	Flanking Active TSS	Liver	Liver

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