Variant report

Variant	rs8054039
Chromosome Location	chr16:47004071-47004072
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	MXI1	chr16:47004018-47004352	HepG2	liver:	n/a	n/a
2	ARID3A	chr16:47004021-47004299	HepG2	liver:	n/a	n/a
3	FOXA1	chr16:47004070-47004418	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
ENSG00000261173	TF binding region

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10459877	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11247542	0.90[EUR][1000 genomes]
rs11859515	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12445492	0.87[EUR][1000 genomes]
rs12447719	0.90[EUR][1000 genomes]
rs12596824	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12719759	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12925296	0.90[EUR][1000 genomes]
rs1362406	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1376734	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[YRI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1551188	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1894886	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1978336	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2058673	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2341648	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35405784	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4246393	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap]
rs4577108	0.90[EUR][1000 genomes]
rs4625742	0.82[EUR][1000 genomes]
rs4966781	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4966794	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4966795	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4966800	0.90[EUR][1000 genomes]
rs4967664	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4967696	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.85[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4967724	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs4967726	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs4967727	0.84[AMR][1000 genomes]
rs4967739	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7189628	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7199379	0.90[EUR][1000 genomes]
rs7199772	0.92[EUR][1000 genomes]
rs7202325	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7203206	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8046142	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8047353	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8052160	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8058144	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8060193	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9745921	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9925290	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9925525	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9927843	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9939872	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1059456	chr16:46463770-47307580	Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
2	nsv1066115	chr16:46463770-47318415	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	nsv1059147	chr16:46500740-47010960	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv542909	chr16:46500740-47010960	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:46977600-47006200	Weak transcription	Stomach Mucosa	stomach
2	chr16:46988000-47004200	Strong transcription	Fetal Thymus	thymus
3	chr16:46988000-47004400	Strong transcription	Primary T cells from cord blood	blood
4	chr16:46988000-47005400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr16:46988000-47005400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr16:46988000-47005600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr16:46988000-47005800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr16:46988200-47005400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr16:46988400-47004600	Strong transcription	Thymus	Thymus
10	chr16:46988400-47005200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr16:46988400-47005800	Strong transcription	Fetal Muscle Leg	muscle
12	chr16:46988400-47006000	Strong transcription	Placenta	Placenta
13	chr16:46988600-47004200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr16:46988600-47005200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr16:46988600-47005200	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr16:46988600-47005400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr16:46988600-47005800	Strong transcription	Fetal Intestine Large	intestine
18	chr16:46988800-47004200	Strong transcription	Fetal Brain Female	brain
19	chr16:46990000-47005800	Strong transcription	Fetal Muscle Trunk	muscle
20	chr16:46990600-47005800	Strong transcription	Sigmoid Colon	Sigmoid Colon
21	chr16:46991000-47004200	Strong transcription	Lung	lung
22	chr16:46994000-47005200	Strong transcription	H1 Cell Line	embryonic stem cell
23	chr16:46994200-47005400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
24	chr16:46994200-47005800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr16:46994400-47005200	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr16:46995200-47005000	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr16:46995200-47005200	Strong transcription	NHEK	skin
28	chr16:46995400-47005200	Strong transcription	Fetal Lung	lung
29	chr16:46995400-47005800	Strong transcription	HSMM	muscle
30	chr16:46995600-47004400	Strong transcription	Fetal Kidney	kidney
31	chr16:46995800-47005400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
32	chr16:46996000-47006000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr16:46996200-47005800	Strong transcription	Fetal Stomach	stomach
34	chr16:46996400-47004600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr16:46996400-47006000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr16:46996600-47004600	Strong transcription	Primary neutrophils fromperipheralblood	blood
37	chr16:46996600-47004800	Strong transcription	H9 Cell Line	embryonic stem cell
38	chr16:46996600-47005600	Strong transcription	Primary B cells from peripheral blood	blood
39	chr16:46996600-47006000	Weak transcription	Right Atrium	heart
40	chr16:46996800-47005200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr16:46996800-47005200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr16:46996800-47005400	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr16:46996800-47005800	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr16:46997000-47005400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr16:46997000-47005600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr16:46997200-47005600	Strong transcription	Osteobl	bone
47	chr16:46997400-47005400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr16:46997400-47005400	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr16:46997600-47005600	Strong transcription	K562	blood
50	chr16:46998600-47004200	Weak transcription	Fetal Heart	heart

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