Variant report

Variant	rs12599703
Chromosome Location	chr16:71319890-71319891
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs13331374	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13336846	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13338238	1.00[CEU][hapmap];0.94[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];1.00[ASN][1000 genomes]
rs13339038	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16970994	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16971009	0.84[CHD][hapmap]
rs2288049	1.00[CEU][hapmap];1.00[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];1.00[ASN][1000 genomes]
rs2303257	0.80[CEU][hapmap];1.00[GIH][hapmap];0.83[EUR][1000 genomes]
rs2356390	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs28409681	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28461749	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28674007	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2883928	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55688282	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55779746	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55918823	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61158660	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61558847	0.80[ASN][1000 genomes]
rs6499496	0.91[CEU][hapmap];0.89[TSI][hapmap]
rs66561786	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66678374	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs68064946	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7184104	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[YRI][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7184118	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs767647	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8055025	0.81[YRI][hapmap]
rs8057700	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9921298	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9924119	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9927680	0.84[ASW][hapmap];0.80[CHB][hapmap];0.89[TSI][hapmap]
rs9927853	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[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	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	nsv482374	chr16:71228600-71401617	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1062426	chr16:71307180-71423400	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12599703	DDX19B	cis	parietal	SCAN
rs12599703	DPEP3	cis	parietal	SCAN
rs12599703	CYB5B	cis	cerebellum	SCAN
rs12599703	FHOD1	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71306600-71322600	Weak transcription	Small Intestine	intestine
2	chr16:71315400-71321800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr16:71315800-71322000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr16:71315800-71322200	Weak transcription	Right Ventricle	heart
5	chr16:71316200-71321000	Strong transcription	HSMM	muscle
6	chr16:71316200-71321400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr16:71316200-71321600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr16:71316600-71321000	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr16:71316600-71322000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr16:71316600-71322600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr16:71316800-71320000	Strong transcription	Brain Germinal Matrix	brain
12	chr16:71316800-71320600	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr16:71316800-71320600	Strong transcription	Duodenum Smooth Muscle	Duodenum
14	chr16:71316800-71320600	Strong transcription	Fetal Lung	lung
15	chr16:71316800-71321000	Strong transcription	Primary B cells from cord blood	blood
16	chr16:71316800-71321000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr16:71316800-71321000	Strong transcription	Left Ventricle	heart
18	chr16:71316800-71321400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr16:71316800-71321600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr16:71316800-71322000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr16:71316800-71322400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr16:71317000-71320000	Strong transcription	Fetal Brain Female	brain
23	chr16:71317000-71320400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr16:71317000-71320600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr16:71317000-71320600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr16:71317000-71320600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr16:71317000-71320600	Strong transcription	Fetal Thymus	thymus
28	chr16:71317000-71320600	Strong transcription	Stomach Smooth Muscle	stomach
29	chr16:71317000-71320800	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr16:71317000-71321000	ZNF genes & repeats	Primary T cells from cord blood	blood
31	chr16:71317000-71321000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr16:71317000-71321000	Strong transcription	Brain Anterior Caudate	brain
33	chr16:71317000-71321000	Strong transcription	Placenta	Placenta
34	chr16:71317000-71321200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr16:71317000-71321200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr16:71317000-71321200	Strong transcription	Liver	Liver
37	chr16:71317000-71321200	Strong transcription	Fetal Muscle Trunk	muscle
38	chr16:71317000-71321400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr16:71317000-71322000	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr16:71317200-71320000	Strong transcription	Brain Cingulate Gyrus	brain
41	chr16:71317200-71320200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr16:71317200-71320400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr16:71317200-71320400	Strong transcription	Brain Hippocampus Middle	brain
44	chr16:71317200-71320400	Strong transcription	Duodenum Mucosa	Duodenum
45	chr16:71317200-71320600	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr16:71317200-71320600	Strong transcription	Muscle Satellite Cultured Cells	--
47	chr16:71317200-71320600	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr16:71317200-71320600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr16:71317200-71320600	Strong transcription	Brain Inferior Temporal Lobe	brain
50	chr16:71317200-71320600	Strong transcription	Fetal Kidney	kidney

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