Variant report

Variant	rs12599890
Chromosome Location	chr16:81496902-81496903
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:81422912..81425576-chr16:81496658..81498919,2	K562	blood:
2	chr16:81489735..81495358-chr16:81495824..81502529,7	MCF-7	breast:
3	chr16:81493353..81497487-chr16:81505659..81509589,4	MCF-7	breast:
4	chr16:81476956..81478649-chr16:81496180..81498094,2	MCF-7	breast:

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs12596103	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[AMR][1000 genomes]
rs12596138	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.83[ASN][1000 genomes]
rs12596605	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12599606	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13330589	1.00[CEU][hapmap]
rs13333580	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs16955379	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[AMR][1000 genomes]
rs16955417	1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[AMR][1000 genomes]
rs2306115	1.00[CEU][hapmap];1.00[AMR][1000 genomes]
rs28517479	0.82[ASN][1000 genomes]
rs28634254	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3803656	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[AMR][1000 genomes]
rs60898915	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9928008	1.00[CEU][hapmap]
rs9930117	0.93[CHB][hapmap]
rs9932863	1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532569	chr16:80980356-81700149	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv1058519	chr16:81177767-81735333	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
3	nsv948448	chr16:81198147-81906766	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	37 gene(s)	inside rSNPs	diseases
4	esv34108	chr16:81469090-81510471	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
5	nsv907010	chr16:81488893-81534790	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:81482000-81507000	Weak transcription	Fetal Heart	heart
2	chr16:81485400-81497000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr16:81485600-81516800	Weak transcription	Hela-S3	cervix
4	chr16:81486000-81500200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr16:81486400-81501800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr16:81486600-81502600	Weak transcription	Fetal Kidney	kidney
7	chr16:81486600-81525200	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr16:81487000-81500000	Weak transcription	Fetal Lung	lung
9	chr16:81487000-81504400	Weak transcription	Fetal Brain Male	brain
10	chr16:81487000-81507200	Weak transcription	Colon Smooth Muscle	Colon
11	chr16:81489000-81499200	Strong transcription	Dnd41	blood
12	chr16:81490600-81509800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr16:81490800-81498800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr16:81490800-81499400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr16:81491000-81500000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr16:81491200-81498800	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr16:81491600-81500000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr16:81491600-81503400	Weak transcription	Rectal Smooth Muscle	rectum
19	chr16:81491800-81498000	Weak transcription	Aorta	Aorta
20	chr16:81491800-81498000	Strong transcription	Fetal Stomach	stomach
21	chr16:81491800-81499600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr16:81492000-81498800	Genic enhancers	HepG2	liver
23	chr16:81492000-81499200	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr16:81492200-81500200	Weak transcription	Fetal Brain Female	brain
25	chr16:81492200-81502000	Weak transcription	Colonic Mucosa	Colon
26	chr16:81492200-81504400	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr16:81492200-81504400	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr16:81492200-81512200	Genic enhancers	A549	lung
29	chr16:81492400-81500000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr16:81492400-81500000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr16:81492400-81500600	Weak transcription	Stomach Smooth Muscle	stomach
32	chr16:81492400-81503000	Weak transcription	NH-A	brain
33	chr16:81492400-81503400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr16:81492600-81506200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr16:81492800-81498400	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr16:81492800-81498400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr16:81492800-81498400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr16:81492800-81504600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr16:81493000-81498800	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr16:81493000-81500600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr16:81493000-81504400	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr16:81493400-81497400	Enhancers	Adipose Nuclei	Adipose
43	chr16:81493600-81498000	Enhancers	Ovary	ovary
44	chr16:81493600-81500000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr16:81493600-81500000	Weak transcription	HMEC	breast
46	chr16:81493600-81500000	Weak transcription	K562	blood
47	chr16:81494000-81499200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr16:81494000-81499200	Weak transcription	Fetal Muscle Leg	muscle
49	chr16:81494200-81499800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr16:81494200-81500200	Weak transcription	Brain Germinal Matrix	brain

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