Variant report

Variant	rs12919092
Chromosome Location	chr16:71446490-71446491
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:21)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:21 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:71446084..71447364-chr16:71575875..71576763,3	MCF-7	breast:
2	chr16:71400881..71402032-chr16:71446303..71446913,3	MCF-7	breast:
3	chr16:71446337..71446843-chr16:71535206..71535723,2	K562	blood:
4	chr16:71446373..71446879-chr16:71455612..71456584,2	K562	blood:
5	chr16:71446209..71447138-chr16:71532022..71532697,2	MCF-7	breast:
6	chr16:71446287..71447211-chr16:71464034..71464697,2	K562	blood:
7	chr16:71035408..71036287-chr16:71446199..71446760,3	MCF-7	breast:
8	chr16:71446366..71447179-chr16:71644599..71645567,3	K562	blood:
9	chr16:71445815..71447496-chr16:71533388..71534585,10	MCF-7	breast:
10	chr16:71446276..71447832-chr16:71533331..71534425,15	K562	blood:
11	chr16:71446456..71447218-chr16:71495594..71496221,2	MCF-7	breast:
12	chr16:71392072..71392977-chr16:71445913..71446834,5	MCF-7	breast:
13	chr16:71406491..71407495-chr16:71445952..71447231,3	MCF-7	breast:
14	chr16:71033153..71034346-chr16:71445929..71447230,11	MCF-7	breast:
15	chr16:71445857..71447501-chr16:71527654..71528626,7	MCF-7	breast:
16	chr16:71446374..71447244-chr16:71571321..71571858,3	K562	blood:
17	chr16:71400999..71401956-chr16:71445867..71446859,3	K562	blood:
18	chr16:71446325..71447209-chr16:71455576..71456210,4	MCF-7	breast:
19	chr16:71034614..71035398-chr16:71445849..71446753,2	MCF-7	breast:
20	chr16:71446140..71447237-chr16:71533352..71534345,5	MCF-7	breast:
21	chr16:71446400..71447280-chr20:56176743..56177607,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000247324	Chromatin interaction
ENSG00000172137	Chromatin interaction
ENSG00000167377	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10468265	0.90[CEU][hapmap]
rs12149254	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12325234	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12444212	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12444714	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12448992	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12918320	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs12922597	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12922830	0.93[EUR][1000 genomes]
rs12934168	1.00[ASN][1000 genomes]
rs16972808	0.90[CEU][hapmap]
rs16973112	0.90[CEU][hapmap]
rs16973190	0.90[CEU][hapmap]
rs17343777	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2033251	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs2052873	0.90[CEU][hapmap]
rs34400718	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35166226	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3886947	0.89[CEU][hapmap]
rs6499520	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs66778248	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7188475	1.00[JPT][hapmap]
rs8051439	0.89[CEU][hapmap]
rs8054221	1.00[ASN][1000 genomes]
rs8056735	0.90[CEU][hapmap]
rs8060176	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
rs12919092	RP11-510M2.10	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71434800-71446600	Weak transcription	Right Atrium	heart
2	chr16:71446000-71446600	Active TSS	iPS-18 Cell Line	embryonic stem cell
3	chr16:71446000-71446800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr16:71446000-71446800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr16:71446000-71446800	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr16:71446000-71446800	Enhancers	Pancreas	Pancrea
7	chr16:71446200-71446600	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr16:71446200-71446600	Bivalent Enhancer	Brain Cingulate Gyrus	brain
9	chr16:71446200-71446600	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
10	chr16:71446200-71446800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr16:71446200-71446800	Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr16:71446200-71446800	Active TSS	HUES64 Cell Line	embryonic stem cell
13	chr16:71446200-71446800	Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr16:71446200-71446800	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr16:71446200-71446800	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr16:71446200-71446800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr16:71446200-71446800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr16:71446200-71446800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr16:71446200-71446800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr16:71446200-71446800	Enhancers	Brain Anterior Caudate	brain
21	chr16:71446200-71446800	Enhancers	Brain Germinal Matrix	brain
22	chr16:71446200-71446800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
23	chr16:71446200-71446800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
24	chr16:71446200-71446800	Bivalent Enhancer	Placenta	Placenta
25	chr16:71446200-71446800	Enhancers	Ovary	ovary
26	chr16:71446200-71446800	Bivalent Enhancer	Stomach Mucosa	stomach
27	chr16:71446200-71446800	Enhancers	HMEC	breast
28	chr16:71446200-71447000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
29	chr16:71446200-71447000	Bivalent Enhancer	HepG2	liver
30	chr16:71446200-71447200	Bivalent Enhancer	Stomach Smooth Muscle	stomach
31	chr16:71446400-71446600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
32	chr16:71446400-71446600	Enhancers	Brain Inferior Temporal Lobe	brain
33	chr16:71446400-71446600	Enhancers	Fetal Brain Female	brain
34	chr16:71446400-71446800	Active TSS	ES-I3 Cell Line	embryonic stem cell
35	chr16:71446400-71446800	Active TSS	H1 Cell Line	embryonic stem cell
36	chr16:71446400-71446800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr16:71446400-71446800	Active TSS	H9 Cell Line	embryonic stem cell
38	chr16:71446400-71446800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr16:71446400-71446800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr16:71446400-71446800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr16:71446400-71446800	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr16:71446400-71446800	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
43	chr16:71446400-71446800	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
44	chr16:71446400-71446800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr16:71446400-71446800	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
46	chr16:71446400-71446800	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
47	chr16:71446400-71446800	Bivalent Enhancer	Adipose Nuclei	Adipose
48	chr16:71446400-71446800	Enhancers	Liver	Liver
49	chr16:71446400-71446800	Bivalent Enhancer	Brain Angular Gyrus	brain
50	chr16:71446400-71446800	Bivalent Enhancer	Fetal Muscle Trunk	muscle

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