Variant report

Variant	rs12708925
Chromosome Location	chr16:72122706-72122707
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:72117692..72119513-chr16:72121450..72123144,2	K562	blood:
2	chr16:72106851..72109339-chr16:72120928..72123034,2	K562	blood:

Variant related genes	Relation type
ENSG00000260252	Chromatin interaction
ENSG00000261701	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10492813	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10492814	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1050361	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1050362	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1050363	0.84[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs11862813	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12325142	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12445586	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12448315	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12708926	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12708927	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12708928	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12924413	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12930702	0.80[ASN][1000 genomes]
rs12932845	0.90[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2072141	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2072142	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2074626	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2074627	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2240243	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2241411	0.87[ASN][1000 genomes]
rs2241412	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2269918	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2303285	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2550035	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2550038	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2854956	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3764311	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3764312	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3764314	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3812986	0.83[ASN][1000 genomes]
rs3852781	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3890860	0.82[AFR][1000 genomes]
rs4788461	0.82[ASN][1000 genomes]
rs6499557	0.81[ASN][1000 genomes]
rs6499559	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6499560	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6499561	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6680	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7190995	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7191127	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7192730	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7194397	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7194668	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7200854	0.81[ASN][1000 genomes]
rs7940	0.89[ASN][1000 genomes]
rs8043606	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8047377	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8051882	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8058609	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8059378	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8059437	0.90[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs8060770	0.83[ASN][1000 genomes]
rs8182213	0.80[ASN][1000 genomes]
rs9925763	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9926156	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9926927	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9928157	0.90[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs9930890	0.88[ASN][1000 genomes]
rs9932062	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9938382	0.80[ASN][1000 genomes]
rs9941087	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9941346	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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
9	esv1808086	chr16:72088669-72128767	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	n/a
10	esv3343168	chr16:72111500-72128436	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12708925	DHX38	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:72106600-72126400	Weak transcription	Small Intestine	intestine
2	chr16:72108000-72126400	Weak transcription	Fetal Heart	heart
3	chr16:72110200-72122800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr16:72117000-72126600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr16:72117800-72124400	Strong transcription	Brain Angular Gyrus	brain
6	chr16:72117800-72124600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr16:72117800-72125000	Strong transcription	Brain Hippocampus Middle	brain
8	chr16:72118000-72124400	Strong transcription	Duodenum Smooth Muscle	Duodenum
9	chr16:72118000-72124600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr16:72118000-72124600	Strong transcription	Brain Germinal Matrix	brain
11	chr16:72118000-72124800	Strong transcription	Adipose Nuclei	Adipose
12	chr16:72118200-72124200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr16:72118200-72124400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr16:72118200-72125000	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr16:72118200-72125200	Strong transcription	Muscle Satellite Cultured Cells	--
16	chr16:72118400-72123600	Strong transcription	Skeletal Muscle Male	skeletal muscle
17	chr16:72118400-72124200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
18	chr16:72118400-72124400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr16:72118400-72124400	Strong transcription	Rectal Smooth Muscle	rectum
20	chr16:72118400-72124600	Strong transcription	Brain Anterior Caudate	brain
21	chr16:72118400-72124600	Strong transcription	Skeletal Muscle Female	skeletal muscle
22	chr16:72118400-72124800	Strong transcription	Fetal Brain Female	brain
23	chr16:72118400-72125200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr16:72118600-72124000	Strong transcription	Colon Smooth Muscle	Colon
25	chr16:72118600-72124200	Strong transcription	HSMM	muscle
26	chr16:72118600-72124400	Strong transcription	Brain Cingulate Gyrus	brain
27	chr16:72118600-72124600	Strong transcription	NHDF-Ad	bronchial
28	chr16:72118600-72124800	Strong transcription	Fetal Intestine Large	intestine
29	chr16:72118800-72124600	Strong transcription	Stomach Smooth Muscle	stomach
30	chr16:72118800-72124800	Strong transcription	Primary T helper cells PMA-I stimulated	--
31	chr16:72118800-72125200	Strong transcription	Rectal Mucosa Donor 31	rectum
32	chr16:72119000-72123000	Strong transcription	HepG2	liver
33	chr16:72119000-72124400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr16:72119000-72124800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr16:72119000-72124800	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr16:72119000-72125000	Strong transcription	Brain Inferior Temporal Lobe	brain
37	chr16:72119200-72123000	Weak transcription	Aorta	Aorta
38	chr16:72119200-72123000	Weak transcription	Stomach Mucosa	stomach
39	chr16:72119200-72123600	Weak transcription	Fetal Brain Male	brain
40	chr16:72119200-72124400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr16:72119200-72124400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr16:72119200-72124400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr16:72119200-72124400	Strong transcription	A549	lung
44	chr16:72119200-72124600	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr16:72119200-72124600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr16:72119200-72124600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr16:72119200-72124600	Strong transcription	Placenta	Placenta
48	chr16:72119200-72124600	Strong transcription	Thymus	Thymus
49	chr16:72119200-72124800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr16:72119200-72125000	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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