Variant report

Variant	rs60745528
Chromosome Location	chr16:48414921-48414922
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:48398121..48402229-chr16:48414201..48420573,11	MCF-7	breast:
2	chr16:48398562..48401765-chr16:48412536..48415889,3	MCF-7	breast:
3	chr16:48411112..48415935-chr16:48417584..48420654,6	MCF-7	breast:
4	chr16:48411748..48415998-chr16:48416243..48420831,11	K562	blood:
5	chr16:48406348..48408797-chr16:48412397..48415717,4	MCF-7	breast:
6	chr16:48396253..48404408-chr16:48411826..48421166,27	K562	blood:

Variant related genes	Relation type
ENSG00000196470	Chromatin interaction

Extended variants
information (count: 144 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10048092	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10221107	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10521167	1.00[ASN][1000 genomes]
rs11076561	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11076562	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11076564	1.00[ASN][1000 genomes]
rs11076565	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11552148	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11859911	1.00[ASN][1000 genomes]
rs11860789	0.97[AFR][1000 genomes];1.00[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	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12103095	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12149230	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12149393	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13330082	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13330105	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13331031	1.00[ASN][1000 genomes]
rs13331250	0.89[AFR][1000 genomes];0.96[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	0.82[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	0.92[AFR][1000 genomes];0.96[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	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1386053	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1545942	0.82[AFR][1000 genomes];0.98[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	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16946039	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16946122	1.00[ASN][1000 genomes]
rs1843647	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2129245	1.00[ASN][1000 genomes]
rs28378550	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28470315	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28515165	1.00[ASN][1000 genomes]
rs28617382	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28716153	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28718435	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28823370	0.83[AFR][1000 genomes];0.95[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	0.83[AFR][1000 genomes];0.95[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	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56385363	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56829365	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58409512	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58938063	1.00[ASN][1000 genomes]
rs59916796	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60431412	1.00[ASN][1000 genomes]
rs60760669	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61122640	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61676712	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6500385	0.96[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	0.97[AFR][1000 genomes];1.00[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	0.96[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	0.97[AFR][1000 genomes];1.00[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	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8045819	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8046408	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8046814	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8047091	0.89[EUR][1000 genomes]
rs8048098	0.96[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	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8051186	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8051205	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8051441	0.93[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	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8054444	0.83[ASN][1000 genomes]
rs8055028	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8055764	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8056692	1.00[ASN][1000 genomes]
rs8056846	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8057475	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8058396	1.00[ASN][1000 genomes]
rs8060780	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8062407	1.00[ASN][1000 genomes]
rs8190	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9302757	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9302758	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9923897	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9924184	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9924497	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9925591	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9925772	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9925935	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9926206	1.00[ASN][1000 genomes]
rs9926363	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9929978	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9931294	0.86[AFR][1000 genomes];0.96[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	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9933211	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9934833	1.00[ASN][1000 genomes]
rs9937882	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9938003	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9938414	1.00[ASN][1000 genomes]
rs9938490	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9938523	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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
12	nsv960007	chr16:48413351-48426696	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs60745528	LONP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:48400600-48417600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr16:48400800-48417800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr16:48403200-48415000	Enhancers	Adipose Nuclei	Adipose
4	chr16:48404800-48417200	Enhancers	Skeletal Muscle Male	skeletal muscle
5	chr16:48406400-48416800	Enhancers	Liver	Liver
6	chr16:48406600-48417200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr16:48407800-48417200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr16:48408000-48415000	Weak transcription	Fetal Muscle Leg	muscle
9	chr16:48408000-48416600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr16:48409000-48417000	Weak transcription	Fetal Kidney	kidney
11	chr16:48409000-48417200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr16:48409200-48416800	Weak transcription	NHDF-Ad	bronchial
13	chr16:48409200-48417000	Weak transcription	NHLF	lung
14	chr16:48409200-48417200	Weak transcription	NH-A	brain
15	chr16:48409200-48417200	Weak transcription	Osteobl	bone
16	chr16:48409400-48416800	Weak transcription	HUVEC	blood vessel
17	chr16:48409400-48417800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr16:48410400-48417600	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr16:48411400-48416200	Enhancers	Sigmoid Colon	Sigmoid Colon
20	chr16:48411600-48415000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr16:48411600-48415000	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr16:48411600-48416200	Enhancers	Placenta	Placenta
23	chr16:48411600-48416400	Weak transcription	HSMM	muscle
24	chr16:48411600-48417400	Enhancers	Primary B cells from cord blood	blood
25	chr16:48411800-48415200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr16:48411800-48417800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr16:48412000-48416800	Enhancers	HepG2	liver
28	chr16:48412000-48417000	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr16:48412200-48415200	Enhancers	Dnd41	blood
30	chr16:48412200-48416600	Enhancers	A549	lung
31	chr16:48412200-48416600	Enhancers	K562	blood
32	chr16:48412400-48415400	Enhancers	Brain Substantia Nigra	brain
33	chr16:48412400-48415600	Enhancers	Spleen	Spleen
34	chr16:48412400-48416000	Enhancers	Brain Cingulate Gyrus	brain
35	chr16:48412400-48416000	Enhancers	Brain Hippocampus Middle	brain
36	chr16:48412400-48416200	Enhancers	Primary B cells from peripheral blood	blood
37	chr16:48412600-48415600	Enhancers	Psoas Muscle	Psoas
38	chr16:48412600-48415800	Enhancers	iPS-18 Cell Line	embryonic stem cell
39	chr16:48412600-48416200	Enhancers	iPS-15b Cell Line	embryonic stem cell
40	chr16:48412600-48416200	Enhancers	Ovary	ovary
41	chr16:48412600-48416200	Enhancers	Pancreas	Pancrea
42	chr16:48412600-48416200	Enhancers	Right Ventricle	heart
43	chr16:48412600-48416400	Enhancers	Left Ventricle	heart
44	chr16:48412600-48416800	Enhancers	Duodenum Mucosa	Duodenum
45	chr16:48413000-48417200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr16:48413200-48415000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr16:48413200-48417800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr16:48413400-48415000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr16:48413400-48416400	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr16:48413400-48416800	Weak transcription	Rectal Smooth Muscle	rectum

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