Variant report

Variant	rs3886947
Chromosome Location	chr16:71483958-71483959
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:71482501..71485257-chr16:71488734..71491145,2	MCF-7	breast:
2	chr16:71482210..71487712-chr16:71492894..71496267,8	K562	blood:
3	chr16:71482572..71485367-chr16:71518078..71520094,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000167377	Chromatin interaction
ENSG00000247324	Chromatin interaction
ENSG00000157429	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10468265	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11866859	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12325234	0.89[CEU][hapmap]
rs12444714	0.89[CEU][hapmap]
rs12918320	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs12919092	0.89[CEU][hapmap]
rs13336809	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16972266	1.00[ASN][1000 genomes]
rs16972805	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16972808	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16973000	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16973112	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16973190	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16973286	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1804984	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2052873	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4258624	1.00[JPT][hapmap]
rs56222754	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57821244	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs59364668	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61171207	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6499520	0.89[CEU][hapmap]
rs6499521	0.83[EUR][1000 genomes]
rs7188021	1.00[ASN][1000 genomes]
rs7197127	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs72791971	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72791974	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72795864	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72795867	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72795869	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72795881	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72797728	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8044168	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs8049040	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs8050135	1.00[ASN][1000 genomes]
rs8051439	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8056735	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9940485	1.00[ASN][1000 genomes]
rs9989376	0.89[EUR][1000 genomes]
rs9989377	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949461	chr16:71196153-71579711	ZNF genes & repeats Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
2	nsv1064435	chr16:71440719-71488771	Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3886947	RP11-510M2.10	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71478200-71487800	ZNF genes & repeats	Adipose Nuclei	Adipose
2	chr16:71479400-71489200	ZNF genes & repeats	Liver	Liver
3	chr16:71479600-71487800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr16:71479600-71488000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
5	chr16:71480000-71485600	ZNF genes & repeats	Fetal Brain Female	brain
6	chr16:71480000-71487000	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
7	chr16:71480400-71485600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr16:71480600-71484600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr16:71480600-71487800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
10	chr16:71480600-71488000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr16:71480600-71488200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr16:71480600-71491000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
13	chr16:71480800-71484800	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr16:71480800-71486000	ZNF genes & repeats	Muscle Satellite Cultured Cells	--
15	chr16:71480800-71486600	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
16	chr16:71480800-71486800	ZNF genes & repeats	Primary T cells from cord blood	blood
17	chr16:71480800-71486800	ZNF genes & repeats	NH-A	brain
18	chr16:71480800-71487200	ZNF genes & repeats	Duodenum Mucosa	Duodenum
19	chr16:71480800-71487600	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
20	chr16:71480800-71488200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr16:71481000-71484400	ZNF genes & repeats	HSMMtube	muscle
22	chr16:71481000-71484800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr16:71481000-71485200	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
24	chr16:71481000-71485200	ZNF genes & repeats	Brain Germinal Matrix	brain
25	chr16:71481000-71485600	ZNF genes & repeats	Right Ventricle	heart
26	chr16:71481000-71486000	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr16:71481000-71486000	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
28	chr16:71481000-71486600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr16:71481000-71486800	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr16:71481000-71487000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
31	chr16:71481000-71487600	ZNF genes & repeats	Psoas Muscle	Psoas
32	chr16:71481000-71487800	ZNF genes & repeats	Fetal Lung	lung
33	chr16:71481000-71489000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr16:71481200-71486000	ZNF genes & repeats	HSMM	muscle
35	chr16:71481200-71487600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr16:71481200-71487800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
37	chr16:71481400-71487200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr16:71481600-71485400	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr16:71481600-71487000	ZNF genes & repeats	Primary B cells from peripheral blood	blood
40	chr16:71481600-71487000	ZNF genes & repeats	NHDF-Ad	bronchial
41	chr16:71481600-71487800	ZNF genes & repeats	Brain Hippocampus Middle	brain
42	chr16:71481600-71490400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
43	chr16:71481600-71493000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr16:71481800-71484400	ZNF genes & repeats	iPS-15b Cell Line	embryonic stem cell
45	chr16:71481800-71484400	ZNF genes & repeats	Primary T killer memory cells from peripheral blood	blood
46	chr16:71481800-71485200	ZNF genes & repeats	Dnd41	blood
47	chr16:71481800-71485600	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
48	chr16:71481800-71486000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
49	chr16:71481800-71486000	ZNF genes & repeats	Fetal Muscle Trunk	muscle
50	chr16:71481800-71486200	ZNF genes & repeats	H1 Cell Line	embryonic stem cell

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