Variant report

Variant	rs12448315
Chromosome Location	chr16:72147242-72147243
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:72143268..72145406-chr16:72145794..72147509,2	MCF-7	breast:

Extended variants
information (count: 68 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10492813	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10492814	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1050361	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1050362	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11075922	0.80[ASN][1000 genomes]
rs11862813	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12325142	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12444701	0.88[ASN][1000 genomes]
rs12445401	0.88[ASN][1000 genomes]
rs12445586	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12708925	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12708926	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12708927	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12708928	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16973716	0.81[ASN][1000 genomes]
rs2072142	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2074626	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2074627	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2240243	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2241412	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2269918	0.81[AMR][1000 genomes]
rs2287997	0.93[ASN][1000 genomes]
rs2303285	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2550038	0.81[EUR][1000 genomes]
rs2854956	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3764311	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3764312	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3764314	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3812987	0.87[ASN][1000 genomes]
rs3852781	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3909542	0.81[AFR][1000 genomes]
rs5472	0.91[EUR][1000 genomes]
rs6416742	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6499559	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6499560	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6499561	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6680	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7184169	0.88[ASN][1000 genomes]
rs7188058	0.82[ASN][1000 genomes]
rs7190995	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7191127	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7192730	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7197453	0.90[EUR][1000 genomes]
rs7197869	0.90[EUR][1000 genomes]
rs8044555	0.89[ASN][1000 genomes]
rs8044868	0.84[AFR][1000 genomes]
rs8047377	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8050238	0.87[ASN][1000 genomes]
rs8051882	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8052408	0.80[ASN][1000 genomes]
rs8058609	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8059378	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8061282	0.88[ASN][1000 genomes]
rs8061459	0.88[ASN][1000 genomes]
rs8062041	0.94[EUR][1000 genomes]
rs9302635	0.93[AFR][1000 genomes]
rs9925763	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9926156	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9926927	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9941087	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948468	chr16:71727571-72651914	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
2	nsv833273	chr16:71971805-72152854	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
3	esv2758430	chr16:71976344-72274347	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	esv2758654	chr16:71976344-72274347	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
5	nsv428329	chr16:71976344-72274347	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
6	nsv1060983	chr16:72074832-72791629	Genic enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
7	nsv534588	chr16:72078262-72287230	ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv1060804	chr16:72078486-72791629	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12448315	DHX38	cis	multi-tissue	Pritchard
rs12448315	DHODH	cis	Artery Tibial	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:72129400-72147800	Strong transcription	Primary T cells from cord blood	blood
2	chr16:72129800-72147600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr16:72129800-72147800	Strong transcription	Sigmoid Colon	Sigmoid Colon
4	chr16:72129800-72148200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr16:72129800-72149000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr16:72130000-72147400	Strong transcription	H1 Cell Line	embryonic stem cell
7	chr16:72130000-72147400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr16:72130000-72147400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr16:72130000-72147400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr16:72130000-72147400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr16:72130000-72147400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr16:72130000-72147400	Strong transcription	Adipose Nuclei	Adipose
13	chr16:72130000-72147400	Strong transcription	Duodenum Mucosa	Duodenum
14	chr16:72130000-72147400	Strong transcription	Fetal Brain Female	brain
15	chr16:72130000-72147400	Strong transcription	Fetal Thymus	thymus
16	chr16:72130000-72147400	Strong transcription	Placenta Amnion	Placenta Amnion
17	chr16:72130000-72147400	Strong transcription	Skeletal Muscle Male	skeletal muscle
18	chr16:72130000-72147600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr16:72130000-72147600	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr16:72130000-72147600	Strong transcription	Primary hematopoietic stem cells	blood
21	chr16:72130000-72147600	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr16:72130000-72147600	Strong transcription	Muscle Satellite Cultured Cells	--
23	chr16:72130000-72147600	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr16:72130000-72147600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr16:72130000-72147600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr16:72130000-72147600	Strong transcription	Duodenum Smooth Muscle	Duodenum
27	chr16:72130000-72147600	Strong transcription	NHLF	lung
28	chr16:72130000-72147800	Strong transcription	Primary T helper cells PMA-I stimulated	--
29	chr16:72130000-72147800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr16:72130000-72147800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr16:72130000-72147800	Strong transcription	Brain Anterior Caudate	brain
32	chr16:72130000-72147800	Strong transcription	Brain Hippocampus Middle	brain
33	chr16:72130000-72147800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr16:72130000-72147800	Strong transcription	Fetal Stomach	stomach
35	chr16:72130000-72147800	Strong transcription	Thymus	Thymus
36	chr16:72130000-72147800	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr16:72130000-72148000	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr16:72130000-72148000	Strong transcription	Brain Cingulate Gyrus	brain
39	chr16:72130000-72148200	Strong transcription	Liver	Liver
40	chr16:72130000-72148200	Strong transcription	Placenta	Placenta
41	chr16:72130200-72147400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr16:72130200-72147400	Strong transcription	Pancreas	Pancrea
43	chr16:72130200-72147600	Strong transcription	Colonic Mucosa	Colon
44	chr16:72130200-72147600	Strong transcription	Lung	lung
45	chr16:72130200-72147600	Strong transcription	Rectal Smooth Muscle	rectum
46	chr16:72130200-72147800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr16:72130200-72147800	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr16:72130200-72148000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr16:72130400-72147400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr16:72130400-72147600	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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