Variant report

Variant	rs893925
Chromosome Location	chr16:30675154-30675155
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	TCF12	chr16:30675112-30675422	GM12878	blood:	n/a	n/a
2	POLR2A	chr16:30675049-30675453	GM12892	blood:	n/a	n/a
3	BATF	chr16:30675119-30675309	GM12878	blood:	n/a	chr16:30675265-30675276
4	POLR2A	chr16:30673388-30675319	GM12878	blood:	n/a	n/a
5	IRF4	chr16:30675066-30675388	GM12878	blood:	n/a	n/a
6	POLR2A	chr16:30674970-30675632	HepG2	liver:	n/a	n/a
7	POLR2A	chr16:30674958-30675277	K562	blood:	n/a	n/a
8	PBX3	chr16:30675147-30675311	GM12878	blood:	n/a	n/a
9	POLR2A	chr16:30675009-30675537	GM12892	blood:	n/a	n/a
10	BATF	chr16:30675129-30675394	GM12878	blood:	n/a	chr16:30675265-30675276
11	POLR2A	chr16:30674991-30675360	GM12878	blood:	n/a	n/a
12	TCF12	chr16:30675129-30675367	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:30665347..30684079-chr16:30697204..30714344,66	MCF-7	breast:
2	chr16:30674519..30676444-chr16:30709698..30711527,2	K562	blood:
3	chr16:30674544..30676988-chr16:30707710..30709714,2	K562	blood:
4	chr16:30673747..30676060-chr16:30719415..30722411,2	MCF-7	breast:

Variant related genes	Relation type
FBRS	TF binding region
ENSG00000080603	Chromatin interaction
ENSG00000206755	Chromatin interaction
ENSG00000222287	Chromatin interaction
ENSG00000261840	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1348039	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1470129	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1530201	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2919428	0.91[YRI][hapmap];1.00[AMR][1000 genomes]
rs2919432	1.00[MKK][hapmap]
rs2972805	1.00[AMR][1000 genomes]
rs2972806	1.00[AMR][1000 genomes]
rs2972808	1.00[MKK][hapmap]
rs2972809	1.00[MKK][hapmap]
rs34838942	1.00[AMR][1000 genomes]
rs35590751	1.00[AMR][1000 genomes]
rs35752464	1.00[AMR][1000 genomes]
rs4889492	1.00[AMR][1000 genomes]
rs4889502	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4889503	1.00[MKK][hapmap]
rs4889505	1.00[MKK][hapmap]
rs4889506	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs55821738	1.00[AMR][1000 genomes]
rs58723456	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59474645	1.00[AMR][1000 genomes]
rs61678005	1.00[AMR][1000 genomes]
rs62057229	1.00[AMR][1000 genomes]
rs6420450	1.00[AMR][1000 genomes]
rs7188789	0.82[YRI][hapmap]
rs7188927	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs7194347	0.81[YRI][hapmap]
rs74015010	1.00[AMR][1000 genomes]
rs74015011	1.00[AMR][1000 genomes]
rs74015012	1.00[AMR][1000 genomes]
rs8048656	1.00[MKK][hapmap]
rs893924	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9925025	0.82[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 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	nsv905727	chr16:30564526-30689696	Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	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
9	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
10	nsv905730	chr16:30667031-30681816	Genic enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
11	nsv905731	chr16:30667031-30685089	Genic enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
12	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
13	esv3442193	chr16:30674901-30676849	Strong transcription Genic enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Enhancers	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:30672200-30675200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr16:30672200-30675400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
3	chr16:30672200-30677000	Genic enhancers	Spleen	Spleen
4	chr16:30672400-30675200	Genic enhancers	Gastric	stomach
5	chr16:30672400-30675400	Genic enhancers	Brain Hippocampus Middle	brain
6	chr16:30672400-30678000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr16:30672600-30675200	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
8	chr16:30672600-30682000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr16:30672800-30675200	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
10	chr16:30672800-30675400	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr16:30672800-30675400	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr16:30672800-30675400	Genic enhancers	Pancreas	Pancrea
13	chr16:30672800-30675400	Genic enhancers	Skeletal Muscle Male	skeletal muscle
14	chr16:30672800-30675400	Genic enhancers	Dnd41	blood
15	chr16:30672800-30675600	Genic enhancers	Primary B cells from peripheral blood	blood
16	chr16:30672800-30676400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr16:30672800-30676400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr16:30672800-30676800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr16:30672800-30678800	Weak transcription	Stomach Mucosa	stomach
20	chr16:30672800-30679600	Strong transcription	HSMMtube	muscle
21	chr16:30672800-30682000	Strong transcription	Lung	lung
22	chr16:30672800-30682000	Strong transcription	A549	lung
23	chr16:30673000-30675200	Genic enhancers	Duodenum Mucosa	Duodenum
24	chr16:30673000-30675400	Genic enhancers	Colonic Mucosa	Colon
25	chr16:30673000-30675400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
26	chr16:30673000-30676200	Genic enhancers	Brain Inferior Temporal Lobe	brain
27	chr16:30673000-30676600	Weak transcription	Psoas Muscle	Psoas
28	chr16:30673000-30677000	Genic enhancers	Primary T cells fromperipheralblood	blood
29	chr16:30673000-30679600	Strong transcription	NHEK	skin
30	chr16:30673000-30682000	Strong transcription	Aorta	Aorta
31	chr16:30673000-30682400	Genic enhancers	Placenta	Placenta
32	chr16:30673000-30682400	Strong transcription	Sigmoid Colon	Sigmoid Colon
33	chr16:30673200-30675200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr16:30673200-30675200	Genic enhancers	Brain Anterior Caudate	brain
35	chr16:30673200-30675400	Genic enhancers	Primary T cells from cord blood	blood
36	chr16:30673200-30675400	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr16:30673200-30675400	Genic enhancers	Colon Smooth Muscle	Colon
38	chr16:30673200-30675400	Strong transcription	Hela-S3	cervix
39	chr16:30673200-30675400	Strong transcription	K562	blood
40	chr16:30673200-30675600	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
41	chr16:30673200-30676000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
42	chr16:30673200-30677600	Strong transcription	Placenta Amnion	Placenta Amnion
43	chr16:30673200-30677800	Strong transcription	Osteobl	bone
44	chr16:30673200-30678200	Weak transcription	Fetal Heart	heart
45	chr16:30673200-30682400	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr16:30673200-30682600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr16:30673200-30682600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr16:30673200-30682600	Strong transcription	Ovary	ovary
49	chr16:30673400-30675200	Genic enhancers	Rectal Mucosa Donor 29	rectum
50	chr16:30673400-30675200	Genic enhancers	NHLF	lung

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