Variant report

Variant	rs9923961
Chromosome Location	chr16:72159675-72159676
allele	C/T
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	SPI1	chr16:72159512-72159872	GM12878	blood:	n/a	chr16:72159703-72159712 chr16:72159700-72159713 chr16:72159704-72159711 chr16:72159666-72159679
2	SPI1	chr16:72159637-72159782	GM12878	blood:	n/a	chr16:72159703-72159712 chr16:72159700-72159713 chr16:72159704-72159711 chr16:72159666-72159679
3	SPI1	chr16:72159570-72159885	GM12891	blood:	n/a	chr16:72159703-72159712 chr16:72159700-72159713 chr16:72159704-72159711 chr16:72159666-72159679
4	ELF1	chr16:72159612-72159980	GM12878	blood:	n/a	n/a
5	SMC3	chr16:72158647-72159874	SK-N-SH	brain:	n/a	chr16:72158956-72158970
6	SPI1	chr16:72159422-72159927	GM12878	blood:	n/a	chr16:72159703-72159712 chr16:72159700-72159713 chr16:72159704-72159711 chr16:72159666-72159679
7	SPI1	chr16:72159598-72159816	GM12891	blood:	n/a	chr16:72159703-72159712 chr16:72159700-72159713 chr16:72159704-72159711 chr16:72159666-72159679
8	ELF1	chr16:72159653-72160027	K562	blood:	n/a	n/a
9	SMC3	chr16:72159552-72159736	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:72159387..72159959-chr16:72182551..72183249,2	MCF-7	breast:

Variant related genes	Relation type
PMFBP1	TF binding region

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1049933	1.00[AMR][1000 genomes]
rs12325171	1.00[AMR][1000 genomes]
rs12325593	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13332560	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs13333207	0.85[AMR][1000 genomes]
rs13334681	1.00[AMR][1000 genomes]
rs13335854	0.85[AMR][1000 genomes]
rs13338949	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16970697	1.00[AMR][1000 genomes]
rs16973640	1.00[AMR][1000 genomes]
rs16973723	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28455724	0.85[AMR][1000 genomes]
rs28483075	0.85[AMR][1000 genomes]
rs28507713	1.00[AMR][1000 genomes]
rs28557204	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28610193	0.85[AMR][1000 genomes]
rs28639994	1.00[AMR][1000 genomes]
rs35184823	1.00[AMR][1000 genomes]
rs56978453	1.00[AMR][1000 genomes]
rs57024912	0.85[AMR][1000 genomes]
rs61074815	1.00[AMR][1000 genomes]
rs7186117	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7186448	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7188150	0.85[AMR][1000 genomes]
rs7188462	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7189506	0.85[AMR][1000 genomes]
rs7189654	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7191270	1.00[AMR][1000 genomes]
rs7191499	1.00[AMR][1000 genomes]
rs7194569	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7202157	0.83[AMR][1000 genomes]
rs7202158	0.83[AMR][1000 genomes]
rs7203195	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73578560	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73580679	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73582412	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8045316	0.85[AMR][1000 genomes]
rs8047881	0.81[AFR][1000 genomes]
rs8051438	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs8052025	1.00[AMR][1000 genomes]
rs8055216	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8056409	0.85[AMR][1000 genomes]
rs8056752	1.00[AMR][1000 genomes]
rs8057379	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8061292	0.85[AMR][1000 genomes]
rs8061439	0.85[AMR][1000 genomes]
rs9921052	0.85[AMR][1000 genomes]
rs9921752	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9925476	1.00[AMR][1000 genomes]
rs9925493	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9932236	1.00[AMR][1000 genomes]
rs9933867	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs9934521	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9940996	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
3	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
4	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
5	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
6	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
7	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

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:72145800-72160400	Weak transcription	HMEC	breast
2	chr16:72146600-72166600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr16:72147000-72164800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr16:72147000-72172200	Weak transcription	Dnd41	blood
5	chr16:72147400-72162200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr16:72147400-72164800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr16:72147600-72165000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr16:72147800-72170000	Weak transcription	Thymus	Thymus
9	chr16:72156200-72160200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr16:72158400-72160200	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr16:72158400-72160600	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr16:72158400-72160600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr16:72158600-72159800	Enhancers	Brain Germinal Matrix	brain
14	chr16:72158600-72159800	Enhancers	Fetal Muscle Trunk	muscle
15	chr16:72158600-72159800	Enhancers	GM12878-XiMat	blood
16	chr16:72158600-72160000	Genic enhancers	Fetal Intestine Small	intestine
17	chr16:72158600-72160600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr16:72158600-72160600	Enhancers	Adipose Nuclei	Adipose
19	chr16:72158600-72160600	Enhancers	Brain Inferior Temporal Lobe	brain
20	chr16:72158800-72160000	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr16:72158800-72160000	Enhancers	Fetal Thymus	thymus
22	chr16:72158800-72160200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr16:72158800-72160600	Enhancers	Brain Angular Gyrus	brain
24	chr16:72159000-72159800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr16:72159000-72159800	Enhancers	Liver	Liver
26	chr16:72159000-72159800	Enhancers	Duodenum Mucosa	Duodenum
27	chr16:72159000-72159800	Enhancers	Fetal Intestine Large	intestine
28	chr16:72159000-72160000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
29	chr16:72159000-72160000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
30	chr16:72159000-72160200	Enhancers	Stomach Mucosa	stomach
31	chr16:72159000-72160400	Enhancers	Rectal Mucosa Donor 31	rectum
32	chr16:72159000-72160600	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr16:72159000-72160800	Enhancers	Rectal Mucosa Donor 29	rectum
34	chr16:72159000-72163000	Weak transcription	Ovary	ovary
35	chr16:72159200-72160000	Enhancers	iPS-15b Cell Line	embryonic stem cell
36	chr16:72159200-72160400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr16:72159200-72160600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr16:72159200-72160600	Enhancers	Brain Hippocampus Middle	brain
39	chr16:72159200-72160800	Enhancers	Brain Anterior Caudate	brain
40	chr16:72159200-72165200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr16:72159400-72159800	Weak transcription	Pancreas	Pancrea
42	chr16:72159400-72160600	Enhancers	Brain Cingulate Gyrus	brain
43	chr16:72159400-72160600	Enhancers	HepG2	liver
44	chr16:72159400-72162800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr16:72159400-72163400	Weak transcription	Fetal Brain Female	brain
46	chr16:72159400-72170200	Weak transcription	Fetal Stomach	stomach
47	chr16:72159600-72159800	Enhancers	ES-I3 Cell Line	embryonic stem cell
48	chr16:72159600-72160000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr16:72159600-72160000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr16:72159600-72160200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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