Variant report

Variant	rs4889504
Chromosome Location	chr16:30762640-30762641
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	POLR2A	chr16:30762551-30762813	HepG2	liver:	n/a	n/a
2	POLR2A	chr16:30762526-30762824	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:30707181..30712037-chr16:30757231..30762842,12	MCF-7	breast:

Variant related genes	Relation type
PHKG2	TF binding region
ENSG00000261840	Chromatin interaction
ENSG00000080603	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10782000	0.94[YRI][hapmap];1.00[AMR][1000 genomes]
rs11150594	1.00[AMR][1000 genomes]
rs11150595	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs11648654	1.00[AMR][1000 genomes]
rs12596375	1.00[ASW][hapmap];1.00[LWK][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12596394	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12598056	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12931844	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12933849	1.00[AMR][1000 genomes]
rs1530203	1.00[ASW][hapmap];0.80[MKK][hapmap];0.83[YRI][hapmap]
rs1550477	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2053426	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2099754	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2099755	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2919427	0.89[ASW][hapmap]
rs2919429	0.87[ASW][hapmap]
rs2919430	1.00[AMR][1000 genomes]
rs2919431	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2919432	0.94[YRI][hapmap];1.00[AMR][1000 genomes]
rs2919433	1.00[AMR][1000 genomes]
rs2972804	1.00[AMR][1000 genomes]
rs2972808	0.82[YRI][hapmap]
rs2972809	0.81[YRI][hapmap]
rs2972815	1.00[AMR][1000 genomes]
rs4268760	0.81[AFR][1000 genomes]
rs4617878	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4889488	1.00[AMR][1000 genomes]
rs4889494	1.00[AMR][1000 genomes]
rs4889500	0.87[ASW][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs4889501	1.00[AMR][1000 genomes]
rs4889503	0.94[YRI][hapmap];1.00[AMR][1000 genomes]
rs4889505	0.94[YRI][hapmap];1.00[AMR][1000 genomes]
rs4889507	0.88[AFR][1000 genomes]
rs4889508	0.88[YRI][hapmap];1.00[AMR][1000 genomes]
rs4889509	1.00[ASW][hapmap];0.95[LWK][hapmap];0.80[MKK][hapmap];1.00[YRI][hapmap]
rs4889510	1.00[AMR][1000 genomes]
rs4889528	1.00[AMR][1000 genomes]
rs55635617	1.00[AMR][1000 genomes]
rs56038936	1.00[AMR][1000 genomes]
rs56209507	1.00[AMR][1000 genomes]
rs57225118	1.00[AMR][1000 genomes]
rs57643871	1.00[AMR][1000 genomes]
rs57877247	1.00[AMR][1000 genomes]
rs6565198	0.83[YRI][hapmap]
rs6565203	1.00[AMR][1000 genomes]
rs6565204	1.00[AMR][1000 genomes]
rs6565205	1.00[AMR][1000 genomes]
rs6565208	0.87[ASW][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes]
rs6565209	1.00[AMR][1000 genomes]
rs6565210	1.00[AMR][1000 genomes]
rs71380412	0.81[AFR][1000 genomes]
rs7185136	0.87[ASW][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs7188077	0.89[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7193412	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7194763	1.00[AMR][1000 genomes]
rs7195583	0.87[ASW][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7195612	0.83[YRI][hapmap];1.00[AMR][1000 genomes]
rs73524581	1.00[AMR][1000 genomes]
rs73524584	1.00[AMR][1000 genomes]
rs73536457	1.00[AMR][1000 genomes]
rs73536466	1.00[AMR][1000 genomes]
rs73536474	1.00[AMR][1000 genomes]
rs73536488	1.00[AMR][1000 genomes]
rs73536498	1.00[AMR][1000 genomes]
rs73536499	1.00[AMR][1000 genomes]
rs8045484	1.00[ASW][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap]
rs8045550	1.00[AMR][1000 genomes]
rs8045624	1.00[ASW][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8046609	1.00[AMR][1000 genomes]
rs8047743	1.00[AMR][1000 genomes]
rs8048656	0.94[YRI][hapmap];1.00[AMR][1000 genomes]
rs8049589	1.00[AMR][1000 genomes]
rs8050578	0.93[YRI][hapmap];1.00[AMR][1000 genomes]
rs8056105	0.96[AFR][1000 genomes]
rs8058475	1.00[AMR][1000 genomes]
rs893926	0.94[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs893927	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9319586	0.87[AFR][1000 genomes]
rs9921630	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9926855	0.91[AFR][1000 genomes]
rs9934046	1.00[AMR][1000 genomes]
rs9941201	1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9941300	0.87[ASW][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062456	chr16:30442166-31253997	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	437 gene(s)	inside rSNPs	diseases
2	nsv542898	chr16:30442166-31253997	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	437 gene(s)	inside rSNPs	diseases
3	nsv469724	chr16:30632445-30840263	Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	143 gene(s)	inside rSNPs	diseases
4	nsv482704	chr16:30632445-30840263	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	143 gene(s)	inside rSNPs	diseases
5	nsv833188	chr16:30632446-30840263	Active TSS Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	143 gene(s)	inside rSNPs	diseases
6	nsv1064134	chr16:30640293-31087327	Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	238 gene(s)	inside rSNPs	diseases
7	nsv905728	chr16:30642867-30928970	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	171 gene(s)	inside rSNPs	diseases
8	nsv905729	chr16:30642867-31247924	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	387 gene(s)	inside rSNPs	diseases
9	esv1825223	chr16:30669091-30971810	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
10	nsv431451	chr16:30682399-31340999	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	350 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:30760000-30772400	Weak transcription	Stomach Mucosa	stomach
2	chr16:30760200-30763800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr16:30760200-30764600	Weak transcription	Aorta	Aorta
4	chr16:30760200-30772200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr16:30760400-30764800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr16:30760400-30772200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr16:30760400-30772200	Weak transcription	Fetal Heart	heart
8	chr16:30760400-30772200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr16:30760400-30772200	Weak transcription	Small Intestine	intestine
10	chr16:30760600-30772200	Weak transcription	Psoas Muscle	Psoas
11	chr16:30760600-30772600	Weak transcription	Right Atrium	heart
12	chr16:30760800-30764000	Weak transcription	Fetal Kidney	kidney
13	chr16:30760800-30771200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr16:30761000-30766000	Weak transcription	Fetal Brain Male	brain
15	chr16:30761000-30769200	Strong transcription	Primary T cells from cord blood	blood
16	chr16:30761000-30769400	Strong transcription	NHEK	skin
17	chr16:30761000-30769400	Strong transcription	Osteobl	bone
18	chr16:30761000-30772000	Strong transcription	Fetal Intestine Small	intestine
19	chr16:30761200-30763200	Strong transcription	A549	lung
20	chr16:30761200-30763400	Strong transcription	HSMM	muscle
21	chr16:30761200-30766800	Strong transcription	NH-A	brain
22	chr16:30761200-30769000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr16:30761200-30769400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr16:30761200-30771200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr16:30761200-30771200	Strong transcription	Placenta Amnion	Placenta Amnion
26	chr16:30761200-30771400	Strong transcription	Fetal Stomach	stomach
27	chr16:30761200-30771600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr16:30761200-30771800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr16:30761200-30771800	Strong transcription	NHLF	lung
30	chr16:30761200-30772000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr16:30761200-30772200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr16:30761400-30763000	Strong transcription	K562	blood
33	chr16:30761400-30768800	Strong transcription	Primary B cells from peripheral blood	blood
34	chr16:30761400-30769000	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr16:30761400-30769000	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr16:30761400-30769000	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr16:30761400-30770000	Strong transcription	Placenta	Placenta
38	chr16:30761400-30771200	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr16:30761400-30771200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr16:30761400-30771400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr16:30761400-30772000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr16:30761600-30763200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr16:30761600-30765800	Strong transcription	Colonic Mucosa	Colon
44	chr16:30761600-30766200	Strong transcription	Fetal Lung	lung
45	chr16:30761600-30768600	Strong transcription	Brain Cingulate Gyrus	brain
46	chr16:30761600-30768600	Strong transcription	Skeletal Muscle Male	skeletal muscle
47	chr16:30761600-30768800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
48	chr16:30761600-30768800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr16:30761600-30769000	Strong transcription	HUES48 Cell Line	embryonic stem cell
50	chr16:30761600-30769400	Strong transcription	Fetal Thymus	thymus

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