Variant report

Variant	rs28439846
Chromosome Location	chr16:75280378-75280379
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:20)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:20 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:75276865-75287749	HepG2	liver:	n/a	n/a
2	POLR2A	chr16:75278032-75286811	HepG2	liver:	n/a	n/a
3	POLR2A	chr16:75277156-75286603	IMR90	lung:	n/a	n/a
4	POLR2A	chr16:75277186-75286167	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr16:75280375-75280669	HepG2	liver:	n/a	n/a
6	POLR2A	chr16:75277560-75287530	HepG2	liver:	n/a	n/a
7	RCOR1	chr16:75278672-75282209	IMR90	lung:	n/a	n/a
8	POLR2A	chr16:75280100-75280750	HUVEC	blood vessel:	n/a	n/a
9	POLR2A	chr16:75277422-75283340	HUVEC	blood vessel:	n/a	n/a
10	CHD2	chr16:75280366-75280562	HepG2	liver:	n/a	n/a
11	POLR2A	chr16:75277805-75281200	HUVEC	blood vessel:	n/a	n/a
12	POLR2A	chr16:75280194-75281154	A549	lung:	n/a	n/a
13	POLR2A	chr16:75280361-75281446	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr16:75277600-75281701	HepG2	liver:	n/a	n/a
15	RAD21	chr16:75280341-75280587	IMR90	lung:	n/a	n/a
16	TEAD4	chr16:75279947-75280454	HepG2	liver:	n/a	n/a
17	POLR2A	chr16:75278353-75280961	HepG2	liver:	n/a	n/a
18	POLR2A	chr16:75277765-75281238	HUVEC	blood vessel:	n/a	n/a
19	POLR2A	chr16:75280180-75288779	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr16:75280333-75280768	HUVEC	blood vessel:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:75279924..75282284-chr16:75466090..75468408,2	K562	blood:
2	chr16:75277872..75280775-chr16:75339667..75341248,2	MCF-7	breast:
3	chr16:75278019..75280837-chr16:75435564..75439238,4	MCF-7	breast:
4	chr16:75278100..75280781-chr16:75467014..75469094,2	MCF-7	breast:
5	chr16:75279429..75281424-chr16:75466908..75468621,2	K562	blood:

No data

Variant related genes	Relation type
BCAR1	TF binding region
ENSG00000153774	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1035539	0.87[ASN][1000 genomes]
rs11645191	0.87[ASN][1000 genomes]
rs13331385	0.90[EUR][1000 genomes]
rs13337017	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13337397	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2287990	0.90[EUR][1000 genomes]
rs28595463	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28690217	0.86[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs2870463	0.85[EUR][1000 genomes]
rs3743614	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3784939	0.83[ASN][1000 genomes]
rs3826110	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56787417	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs59067758	0.81[ASN][1000 genomes]
rs60470336	0.85[EUR][1000 genomes]
rs60852020	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs60879082	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61634868	0.85[EUR][1000 genomes]
rs6564232	0.85[EUR][1000 genomes]
rs6564233	0.85[EUR][1000 genomes]
rs6564234	0.85[EUR][1000 genomes]
rs6564236	0.85[EUR][1000 genomes]
rs6564237	0.85[EUR][1000 genomes]
rs66473537	0.85[EUR][1000 genomes]
rs66535165	0.85[EUR][1000 genomes]
rs66881382	0.85[EUR][1000 genomes]
rs67478528	0.85[EUR][1000 genomes]
rs7185352	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7197389	0.85[EUR][1000 genomes]
rs7197746	0.85[EUR][1000 genomes]
rs7202844	0.85[EUR][1000 genomes]
rs7202858	0.83[EUR][1000 genomes]
rs7202877	0.85[EUR][1000 genomes]
rs72802372	0.85[EUR][1000 genomes]
rs72802375	0.85[EUR][1000 genomes]
rs72804106	0.99[EUR][1000 genomes]
rs73605136	0.83[EUR][1000 genomes]
rs73605139	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8046145	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8048529	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8053595	0.85[EUR][1000 genomes]
rs8054218	0.85[EUR][1000 genomes]
rs8063014	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9921586	0.86[EUR][1000 genomes]
rs9940370	0.85[EUR][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	nsv1061095	chr16:74519718-75407020	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv532560	chr16:74692406-75411912	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
3	nsv916502	chr16:74845880-75732365	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	131 gene(s)	inside rSNPs	diseases
4	nsv1056082	chr16:75004990-75295847	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv833282	chr16:75154171-75330634	Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
6	nsv516504	chr16:75223491-75306402	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
7	nsv523405	chr16:75227969-75342846	Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
8	esv1806781	chr16:75235390-75307470	Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
9	nsv906909	chr16:75236154-75316074	Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
10	esv1792587	chr16:75237936-75305783	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
11	nsv906910	chr16:75251299-75316074	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
12	nsv906911	chr16:75252526-75296247	Active TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
13	nsv906912	chr16:75252526-75320827	Flanking Active TSS Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
14	esv1813349	chr16:75257361-75302684	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
15	nsv931939	chr16:75261354-75765025	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
16	nsv906913	chr16:75267743-75306402	Genic enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases
17	nsv471095	chr16:75269533-75320827	Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases
18	esv1843498	chr16:75271642-75296844	Genic enhancers Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases
19	nsv978002	chr16:75274402-75288324	Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:75269600-75280600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr16:75276800-75283400	Enhancers	NHDF-Ad	bronchial
3	chr16:75276800-75283800	Enhancers	Left Ventricle	heart
4	chr16:75277000-75281400	Enhancers	Brain Angular Gyrus	brain
5	chr16:75277000-75283400	Genic enhancers	Fetal Intestine Small	intestine
6	chr16:75277200-75281600	Genic enhancers	Fetal Stomach	stomach
7	chr16:75277200-75284200	Enhancers	Spleen	Spleen
8	chr16:75277400-75281800	Enhancers	Adipose Nuclei	Adipose
9	chr16:75277400-75281800	Enhancers	Stomach Mucosa	stomach
10	chr16:75277400-75283400	Enhancers	Colon Smooth Muscle	Colon
11	chr16:75277600-75281200	Enhancers	Esophagus	oesophagus
12	chr16:75277600-75281400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr16:75277600-75281600	Flanking Active TSS	Stomach Smooth Muscle	stomach
14	chr16:75277600-75283200	Enhancers	Psoas Muscle	Psoas
15	chr16:75277600-75283600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr16:75277600-75283800	Enhancers	H1 Cell Line	embryonic stem cell
17	chr16:75277600-75283800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr16:75277600-75283800	Enhancers	Ovary	ovary
19	chr16:75277600-75284000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr16:75277600-75284000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr16:75277600-75284000	Enhancers	Right Atrium	heart
22	chr16:75277600-75284400	Enhancers	Fetal Lung	lung
23	chr16:75277800-75280800	Enhancers	Lung	lung
24	chr16:75277800-75281800	Enhancers	HSMMtube	muscle
25	chr16:75277800-75282800	Enhancers	Rectal Mucosa Donor 31	rectum
26	chr16:75277800-75284200	Enhancers	Liver	Liver
27	chr16:75278000-75280400	Enhancers	Fetal Muscle Trunk	muscle
28	chr16:75278000-75280600	Enhancers	Fetal Brain Male	brain
29	chr16:75278000-75281400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr16:75278000-75282400	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr16:75278000-75282600	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr16:75278000-75284000	Enhancers	Placenta Amnion	Placenta Amnion
33	chr16:75278200-75280800	Enhancers	Brain Cingulate Gyrus	brain
34	chr16:75278200-75283800	Enhancers	Pancreas	Pancrea
35	chr16:75278200-75284800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
36	chr16:75278400-75281000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr16:75278400-75281200	Enhancers	iPS-18 Cell Line	embryonic stem cell
38	chr16:75278400-75281200	Enhancers	Fetal Muscle Leg	muscle
39	chr16:75278400-75282000	Enhancers	iPS-20b Cell Line	embryonic stem cell
40	chr16:75278600-75280400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr16:75278600-75280400	Enhancers	Fetal Kidney	kidney
42	chr16:75278600-75281000	Enhancers	Fetal Intestine Large	intestine
43	chr16:75278600-75281000	Flanking Active TSS	Hela-S3	cervix
44	chr16:75278600-75284000	Enhancers	Sigmoid Colon	Sigmoid Colon
45	chr16:75278800-75280800	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr16:75278800-75282200	Enhancers	Rectal Mucosa Donor 29	rectum
47	chr16:75278800-75282800	Enhancers	NH-A	brain
48	chr16:75278800-75284000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr16:75279000-75282800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr16:75279000-75283800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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