Variant report

Variant	rs4889571
Chromosome Location	chr16:30949047-30949048
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:30948680-30949092	K562	blood:	n/a	n/a
2	POLR2A	chr16:30948477-30949490	HL-60	blood:	n/a	n/a
3	POLR2A	chr16:30948274-30949415	HL-60	blood:	n/a	n/a
4	SPI1	chr16:30948899-30949375	HL-60	blood:	n/a	n/a
5	POLR2A	chr16:30948830-30949209	GM12878	blood:	n/a	n/a
6	POLR2A	chr16:30948306-30949246	GM12878	blood:	n/a	n/a
7	POLR2A	chr16:30948986-30949159	MCF-7	breast:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:30946645..30949568-chr16:30950712..30953448,2	MCF-7	breast:
2	chr16:30947629..30950363-chr16:30951852..30955224,3	K562	blood:
3	chr16:30947459..30949066-chr16:30961227..30963883,2	MCF-7	breast:
4	chr16:30946735..30949236-chr16:30950028..30951907,2	MCF-7	breast:
5	chr16:30941276..30943882-chr16:30947649..30950883,3	K562	blood:
6	chr16:30934783..30936608-chr16:30947916..30950707,2	MCF-7	breast:
7	chr16:30941864..30943942-chr16:30947388..30950246,2	MCF-7	breast:
8	chr16:30935980..30940118-chr16:30945384..30950670,5	K562	blood:

No data

Variant related genes	Relation type
FBXL19	TF binding region
ENSG00000099364	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1046276	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10782001	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10782002	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11076	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11150600	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11150601	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11640534	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11649653	0.87[ASN][1000 genomes]
rs12445568	0.81[EUR][1000 genomes]
rs12599631	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12716978	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12917722	1.00[ASN][1000 genomes]
rs12924903	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12928852	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12930545	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12930657	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12931046	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12934900	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13336347	1.00[ASN][1000 genomes]
rs13708	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1458202	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1870293	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2054213	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2199036	0.81[EUR][1000 genomes]
rs2305880	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2305884	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28360557	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34873012	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35675346	0.90[ASN][1000 genomes]
rs35733741	1.00[ASN][1000 genomes]
rs3813020	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4502227	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4889514	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4889525	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4889599	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4889603	0.95[ASN][1000 genomes]
rs4889604	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4889685	0.94[EUR][1000 genomes]
rs62055866	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6950	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7185007	0.84[ASN][1000 genomes]
rs7200879	0.90[ASN][1000 genomes]
rs7203999	0.81[EUR][1000 genomes]
rs7204459	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7206511	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72799341	0.90[ASN][1000 genomes]
rs8046707	0.87[ASN][1000 genomes]
rs8050588	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8052245	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8060857	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8062719	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs897986	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9319588	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9938050	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9938550	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 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	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
4	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
5	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
6	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
7	nsv905733	chr16:30796919-31004812	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	112 gene(s)	inside rSNPs	diseases
8	nsv869652	chr16:30799471-30951038	Bivalent Enhancer Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	70 gene(s)	inside rSNPs	diseases
9	nsv833189	chr16:30819708-30960795	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	79 gene(s)	inside rSNPs	diseases
10	nsv833190	chr16:30845051-31007863	Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	105 gene(s)	inside rSNPs	diseases
11	nsv833191	chr16:30864242-31048051	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	115 gene(s)	inside rSNPs	diseases
12	nsv905734	chr16:30877544-31191482	Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
13	nsv905735	chr16:30890538-31247924	Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	264 gene(s)	inside rSNPs	diseases
14	nsv905736	chr16:30900235-30995528	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
15	nsv905737	chr16:30900235-31014179	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Strong transcription 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	95 gene(s)	inside rSNPs	diseases
16	nsv457483	chr16:30903679-31191482	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Strong transcription Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	253 gene(s)	inside rSNPs	diseases
17	nsv571820	chr16:30903679-31191482	Enhancers Genic enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	253 gene(s)	inside rSNPs	diseases
18	nsv905738	chr16:30906274-30973926	Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
19	esv1797877	chr16:30948643-31188432	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4889571	HSD3B7	cis	Esophagus Mucosa	GTEx
rs4889571	HSD3B7	cis	Skin Sun Exposed Lower leg	GTEx
rs4889571	RP11-196G11.2	cis	Muscle Skeletal	GTEx
rs4889571	HSD3B7	cis	Muscle Skeletal	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:30936000-30953400	Weak transcription	Right Atrium	heart
2	chr16:30936400-30955200	Weak transcription	Fetal Kidney	kidney
3	chr16:30936400-30955800	Weak transcription	Small Intestine	intestine
4	chr16:30936600-30952800	Weak transcription	Hela-S3	cervix
5	chr16:30936600-30953000	Weak transcription	Stomach Mucosa	stomach
6	chr16:30937400-30949400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr16:30937600-30951800	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr16:30937600-30958600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr16:30937800-30953000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr16:30938200-30953000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr16:30939200-30949600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr16:30939200-30953000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr16:30939400-30949400	Strong transcription	Cortex derived primary cultured neurospheres	brain
14	chr16:30939400-30958800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr16:30939600-30949400	Strong transcription	Fetal Stomach	stomach
16	chr16:30939600-30949800	Strong transcription	Fetal Brain Female	brain
17	chr16:30939600-30950400	Strong transcription	H1 Cell Line	embryonic stem cell
18	chr16:30939600-30959000	Strong transcription	Brain Germinal Matrix	brain
19	chr16:30940000-30949200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr16:30940000-30953000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr16:30940200-30949200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr16:30940400-30951000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr16:30940600-30950000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr16:30942400-30953200	Weak transcription	Colonic Mucosa	Colon
25	chr16:30942400-30959600	Weak transcription	Psoas Muscle	Psoas
26	chr16:30942800-30953000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr16:30943200-30952200	Weak transcription	GM12878-XiMat	blood
28	chr16:30943800-30951000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr16:30943800-30952800	Weak transcription	Brain Angular Gyrus	brain
30	chr16:30943800-30955000	Weak transcription	Fetal Brain Male	brain
31	chr16:30944000-30951000	Weak transcription	NH-A	brain
32	chr16:30944000-30951400	Strong transcription	Fetal Intestine Large	intestine
33	chr16:30944000-30951800	Weak transcription	HUVEC	blood vessel
34	chr16:30944000-30952800	Strong transcription	Fetal Intestine Small	intestine
35	chr16:30944000-30953000	Weak transcription	Colon Smooth Muscle	Colon
36	chr16:30944000-30953000	Weak transcription	NHDF-Ad	bronchial
37	chr16:30944000-30953200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr16:30944000-30953400	Weak transcription	Liver	Liver
39	chr16:30944200-30951000	Weak transcription	HMEC	breast
40	chr16:30944200-30953200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr16:30944200-30955600	Weak transcription	Aorta	Aorta
42	chr16:30944400-30951800	Weak transcription	Brain Hippocampus Middle	brain
43	chr16:30944400-30953400	Weak transcription	Left Ventricle	heart
44	chr16:30944400-30955000	Weak transcription	Primary T cells from cord blood	blood
45	chr16:30944600-30953000	Weak transcription	Adipose Nuclei	Adipose
46	chr16:30945400-30950000	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr16:30945400-30952000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr16:30945400-30952200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr16:30945600-30949200	Strong transcription	NHEK	skin
50	chr16:30946000-30949200	Strong transcription	Fetal Lung	lung

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