Variant report

Variant	rs1105407
Chromosome Location	chr16:48466286-48466287
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:48417972..48420072-chr16:48465753..48468284,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196470	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10048092	0.83[CEU][hapmap]
rs10221107	0.83[CEU][hapmap]
rs11076565	0.83[CEU][hapmap]
rs11552148	0.83[CEU][hapmap]
rs11862480	1.00[CHB][hapmap]
rs16946038	0.84[CEU][hapmap]
rs16946039	0.83[CEU][hapmap]
rs28617382	0.83[CEU][hapmap]
rs6500385	0.83[CEU][hapmap]
rs8046408	0.83[CEU][hapmap]
rs8051441	0.83[CEU][hapmap]
rs8054314	0.83[CEU][hapmap]
rs8055028	0.83[CEU][hapmap]
rs8190	0.83[CEU][hapmap]
rs9302758	0.83[CEU][hapmap]
rs9925772	0.83[CEU][hapmap]
rs9938490	0.83[CEU][hapmap]
rs9940038	0.83[CEU][hapmap]

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	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
4	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
5	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
6	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
7	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
8	nsv1056931	chr16:48417388-48482594	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
9	nsv542918	chr16:48417388-48482594	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
10	esv1800739	chr16:48418505-48560315	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
11	nsv428658	chr16:48438656-48587750	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1105407	LONP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:48461200-48469000	Weak transcription	Right Atrium	heart
2	chr16:48461800-48468800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr16:48462800-48468800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr16:48464000-48470000	Enhancers	Primary B cells from peripheral blood	blood
5	chr16:48465200-48468400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr16:48465600-48466600	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr16:48465600-48466600	Flanking Active TSS	GM12878-XiMat	blood
8	chr16:48465600-48468400	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr16:48465600-48470200	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr16:48465800-48466400	Flanking Active TSS	Primary B cells from cord blood	blood
11	chr16:48465800-48466800	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr16:48465800-48466800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
13	chr16:48465800-48469800	Enhancers	Primary hematopoietic stem cells	blood
14	chr16:48466000-48466400	Enhancers	H9 Cell Line	embryonic stem cell
15	chr16:48466000-48466400	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr16:48466000-48466400	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr16:48466000-48466400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr16:48466000-48466400	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr16:48466000-48466400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr16:48466000-48466400	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr16:48466000-48466600	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr16:48466000-48466600	Enhancers	iPS-18 Cell Line	embryonic stem cell
23	chr16:48466000-48466600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr16:48466000-48466600	Enhancers	Rectal Mucosa Donor 29	rectum
25	chr16:48466000-48467800	Enhancers	Spleen	Spleen
26	chr16:48466000-48469400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr16:48466200-48466400	Enhancers	Duodenum Mucosa	Duodenum
28	chr16:48466200-48466400	Enhancers	Left Ventricle	heart
29	chr16:48466200-48466400	Enhancers	Right Ventricle	heart
30	chr16:48466200-48466600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
31	chr16:48466200-48466600	Enhancers	Adipose Nuclei	Adipose
32	chr16:48466200-48466600	Enhancers	Pancreas	Pancrea
33	chr16:48466200-48466600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
34	chr16:48466200-48470200	Enhancers	Placenta	Placenta

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