Variant report

Variant	rs28378550
Chromosome Location	chr16:48404458-48404459
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:48403583-48404487	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:48404265..48407102-chr16:48407318..48409979,3	K562	blood:
2	chr16:48402282..48407133-chr16:48417266..48420023,6	MCF-7	breast:
3	chr16:48394386..48397097-chr16:48404388..48407355,2	K562	blood:

Variant related genes	Relation type
SIAH1	TF binding region
ENSG00000196470	Chromatin interaction

Extended variants
information (count: 143 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:132)

rs_ID	r²[population]
rs10048092	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10221107	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10521167	1.00[ASN][1000 genomes]
rs11076561	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11076562	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11076564	1.00[ASN][1000 genomes]
rs11076565	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11552148	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11859911	1.00[ASN][1000 genomes]
rs11860789	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11861348	1.00[ASN][1000 genomes]
rs11861379	1.00[ASN][1000 genomes]
rs11863414	1.00[ASN][1000 genomes]
rs11865596	1.00[ASN][1000 genomes]
rs11866225	1.00[ASN][1000 genomes]
rs11866529	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12103095	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12149230	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12149393	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13330082	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13330105	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13331031	1.00[ASN][1000 genomes]
rs13331250	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13332304	1.00[ASN][1000 genomes]
rs13334052	1.00[ASN][1000 genomes]
rs13336264	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13336542	1.00[ASN][1000 genomes]
rs13336625	1.00[ASN][1000 genomes]
rs13336759	1.00[ASN][1000 genomes]
rs13336771	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13337955	1.00[ASN][1000 genomes]
rs13338105	1.00[ASN][1000 genomes]
rs13338978	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1386053	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1545942	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16945988	1.00[ASN][1000 genomes]
rs16945990	1.00[ASN][1000 genomes]
rs16946006	1.00[ASN][1000 genomes]
rs16946011	1.00[ASN][1000 genomes]
rs16946014	1.00[ASN][1000 genomes]
rs16946038	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16946039	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16946122	1.00[ASN][1000 genomes]
rs1843647	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2129245	1.00[ASN][1000 genomes]
rs28470315	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28515165	1.00[ASN][1000 genomes]
rs28617382	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28716153	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28718435	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28823370	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28842015	1.00[ASN][1000 genomes]
rs28849445	1.00[ASN][1000 genomes]
rs34135802	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4325548	1.00[ASN][1000 genomes]
rs4340327	1.00[ASN][1000 genomes]
rs4528570	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56385363	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56829365	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58409512	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58938063	1.00[ASN][1000 genomes]
rs59916796	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60431412	1.00[ASN][1000 genomes]
rs60745528	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60760669	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61122640	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61676712	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6500385	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs70973926	1.00[ASN][1000 genomes]
rs7184452	1.00[ASN][1000 genomes]
rs7186777	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7186982	1.00[ASN][1000 genomes]
rs7187233	0.83[EUR][1000 genomes]
rs7202089	1.00[ASN][1000 genomes]
rs7203432	1.00[ASN][1000 genomes]
rs7203659	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7206909	0.81[EUR][1000 genomes]
rs73555628	1.00[ASN][1000 genomes]
rs73555630	1.00[ASN][1000 genomes]
rs73555643	1.00[ASN][1000 genomes]
rs73562063	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7359477	1.00[ASN][1000 genomes]
rs8043685	1.00[ASN][1000 genomes]
rs8043751	1.00[ASN][1000 genomes]
rs8043803	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8045819	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8046408	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8046814	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8047091	0.89[EUR][1000 genomes]
rs8048098	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8049398	1.00[ASN][1000 genomes]
rs8050120	0.80[EUR][1000 genomes]
rs8051016	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8051186	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8051205	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8051441	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8051546	1.00[ASN][1000 genomes]
rs8051852	1.00[ASN][1000 genomes]
rs8054117	1.00[ASN][1000 genomes]
rs8054314	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8054444	0.83[ASN][1000 genomes]
rs8055028	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8055764	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8056692	1.00[ASN][1000 genomes]
rs8056846	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8057475	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8058396	1.00[ASN][1000 genomes]
rs8060780	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8062407	1.00[ASN][1000 genomes]
rs8190	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9302757	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9302758	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9923897	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9924184	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9924497	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9925591	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9925772	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9925935	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9926206	1.00[ASN][1000 genomes]
rs9926363	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9929978	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9931294	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9932328	1.00[ASN][1000 genomes]
rs9932850	0.90[EUR][1000 genomes]
rs9932964	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9933211	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9934833	1.00[ASN][1000 genomes]
rs9937882	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9938003	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9938414	1.00[ASN][1000 genomes]
rs9938490	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9938523	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1061316	chr16:48264175-48594219	Weak transcription Strong transcription Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	esv1821072	chr16:48268318-48504364	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv833219	chr16:48290595-48459301	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv1061708	chr16:48304343-48482594	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv542917	chr16:48304343-48482594	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	esv2758424	chr16:48329437-48479754	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	esv2758645	chr16:48329437-48479754	ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
8	esv1837150	chr16:48375777-48470715	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
9	esv1802902	chr16:48394626-48419662	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	22 gene(s)	inside rSNPs	diseases
10	esv1836876	chr16:48395527-48459558	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
11	esv1842331	chr16:48395527-48459558	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28378550	LONP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:48400200-48409000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr16:48400400-48404800	Weak transcription	Pancreas	Pancrea
3	chr16:48400600-48417600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr16:48400800-48406600	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr16:48400800-48417800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr16:48401000-48404600	Weak transcription	Lung	lung
7	chr16:48401000-48404600	Weak transcription	Ovary	ovary
8	chr16:48401000-48405000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr16:48401000-48406800	Weak transcription	Right Atrium	heart
10	chr16:48401000-48407400	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr16:48401000-48412600	Weak transcription	Thymus	Thymus
12	chr16:48401200-48404600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr16:48401200-48404600	Weak transcription	Left Ventricle	heart
14	chr16:48401200-48409000	Weak transcription	Gastric	stomach
15	chr16:48401400-48406800	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr16:48401400-48406800	Weak transcription	Fetal Muscle Leg	muscle
17	chr16:48401400-48407000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr16:48401400-48407000	Weak transcription	Fetal Kidney	kidney
19	chr16:48401400-48407400	Weak transcription	Aorta	Aorta
20	chr16:48401400-48408400	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr16:48401400-48408400	Weak transcription	Stomach Smooth Muscle	stomach
22	chr16:48401600-48406200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr16:48401600-48406400	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr16:48401600-48406600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr16:48401600-48407400	Weak transcription	HSMM	muscle
26	chr16:48401600-48407600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr16:48401600-48407800	Weak transcription	Duodenum Mucosa	Duodenum
28	chr16:48401600-48412400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr16:48401800-48404800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr16:48401800-48405000	Weak transcription	Fetal Heart	heart
31	chr16:48401800-48405000	Weak transcription	Fetal Lung	lung
32	chr16:48401800-48405200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr16:48401800-48405200	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr16:48401800-48405200	Weak transcription	Osteobl	bone
35	chr16:48401800-48405600	Weak transcription	Colon Smooth Muscle	Colon
36	chr16:48401800-48405600	Weak transcription	Fetal Brain Male	brain
37	chr16:48401800-48405600	Weak transcription	Fetal Brain Female	brain
38	chr16:48401800-48405800	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr16:48401800-48406400	Weak transcription	Liver	Liver
40	chr16:48401800-48406400	Weak transcription	Brain Germinal Matrix	brain
41	chr16:48401800-48406600	Weak transcription	Small Intestine	intestine
42	chr16:48401800-48406800	Weak transcription	HSMMtube	muscle
43	chr16:48401800-48407200	Weak transcription	Rectal Smooth Muscle	rectum
44	chr16:48401800-48407400	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr16:48401800-48407400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr16:48401800-48407400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr16:48401800-48407600	Weak transcription	Primary hematopoietic stem cells	blood
48	chr16:48401800-48408000	Weak transcription	Stomach Mucosa	stomach
49	chr16:48401800-48408600	Weak transcription	Primary T cells from cord blood	blood
50	chr16:48401800-48408800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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