Variant report

Variant	rs28690217
Chromosome Location	chr16:75260329-75260330
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:37)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:37 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:75260039-75260358	HCT-116	colon:	n/a	n/a
2	POLR2A	chr16:75259983-75262273	U87	brain:	n/a	n/a
3	POLR2A	chr16:75259576-75260342	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr16:75259983-75262388	U87	brain:	n/a	n/a
5	POLR2A	chr16:75259546-75262840	U87	brain:	n/a	n/a
6	POLR2A	chr16:75260070-75260338	ECC-1	luminal epithelium:	n/a	n/a
7	POLR2A	chr16:75259562-75260347	A549	lung:	n/a	n/a
8	POLR2A	chr16:75259865-75263266	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr16:75258283-75261725	MCF-7	breast:	n/a	n/a
10	BCL3	chr16:75260021-75261939	A549	lung:	n/a	n/a
11	POLR2A	chr16:75259966-75262915	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr16:75258107-75264329	HUVEC	blood vessel:	n/a	n/a
13	JUND	chr16:75259970-75261197	A549	lung:	n/a	n/a
14	POLR2A	chr16:75259551-75260383	HUVEC	blood vessel:	n/a	n/a
15	POLR2A	chr16:75259688-75263272	A549	lung:	n/a	n/a
16	POLR2A	chr16:75260040-75260337	H1-hESC	embryonic stem cell:	n/a	n/a
17	BCL3	chr16:75259937-75260365	A549	lung:	n/a	n/a
18	FOSL2	chr16:75259966-75260340	HepG2	liver:	n/a	n/a
19	POLR2A	chr16:75258204-75262150	PANC-1	pancreas:	n/a	n/a
20	POLR2A	chr16:75260059-75260329	A549	lung:	n/a	n/a
21	POLR2A	chr16:75258031-75262846	U87	brain:	n/a	n/a
22	POLR2A	chr16:75260063-75261925	HUVEC	blood vessel:	n/a	n/a
23	POLR2A	chr16:75259802-75261977	IMR90	lung:	n/a	n/a
24	POLR2A	chr16:75259761-75264131	HepG2	liver:	n/a	n/a
25	POLR2A	chr16:75259983-75262369	PFSK-1	brain:	n/a	n/a
26	POLR2A	chr16:75260066-75263057	HepG2	liver:	n/a	n/a
27	POLR2A	chr16:75257216-75264212	HUVEC	blood vessel:	n/a	n/a
28	POLR2A	chr16:75258076-75263377	HUVEC	blood vessel:	n/a	n/a
29	PBX3	chr16:75259558-75260349	SK-N-SH	brain:	n/a	n/a
30	POLR2A	chr16:75260047-75260331	HepG2	liver:	n/a	n/a
31	POLR2A	chr16:75260129-75261772	GM12891	blood:	n/a	n/a
32	POLR2A	chr16:75257971-75261698	SK-N-SH	brain:	n/a	n/a
33	POLR2A	chr16:75259959-75260361	ProgFib	skin:	n/a	n/a
34	POLR2A	chr16:75258064-75263524	PANC-1	pancreas:	n/a	n/a
35	POLR2A	chr16:75260031-75260364	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr16:75259547-75263875	H1-hESC	embryonic stem cell:	n/a	n/a
37	POLR2A	chr16:75258033-75265096	HUVEC	blood vessel:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr16:75259564..75261896-chr16:75284703..75287235,2	K562	blood:
2	chr16:75182251..75184924-chr16:75259664..75261950,2	MCF-7	breast:
3	chr16:75239816..75243837-chr16:75256696..75260507,7	MCF-7	breast:
4	chr16:75260096..75262598-chr16:75274071..75277051,2	K562	blood:
5	chr16:75258373..75260591-chr16:75260652..75263277,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CTRB1-1	chr16:75259972-75260623	NONHSAT143724

No data

Variant related genes	Relation type
ENSG00000240338	TF binding region
ENSG00000168928	Chromatin interaction
ENSG00000050820	Chromatin interaction
ENSG00000240338	Chromatin interaction
ENSG00000184517	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs13331385	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13337017	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs13337397	0.89[EUR][1000 genomes]
rs2287990	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28439846	0.86[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs28595463	0.86[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs2870463	0.94[EUR][1000 genomes]
rs3743614	0.90[EUR][1000 genomes]
rs3826110	0.90[EUR][1000 genomes]
rs56787417	0.86[EUR][1000 genomes]
rs60470336	0.94[EUR][1000 genomes]
rs60852020	0.89[EUR][1000 genomes]
rs60879082	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs61634868	0.94[EUR][1000 genomes]
rs6564232	0.94[EUR][1000 genomes]
rs6564233	0.94[EUR][1000 genomes]
rs6564234	0.94[EUR][1000 genomes]
rs6564235	0.89[EUR][1000 genomes]
rs6564236	0.94[EUR][1000 genomes]
rs6564237	0.94[EUR][1000 genomes]
rs66473537	0.94[EUR][1000 genomes]
rs66535165	0.94[EUR][1000 genomes]
rs66881382	0.94[EUR][1000 genomes]
rs67478528	0.94[EUR][1000 genomes]
rs7185352	0.86[EUR][1000 genomes]
rs7195852	0.88[EUR][1000 genomes]
rs7197389	0.94[EUR][1000 genomes]
rs7197746	0.94[EUR][1000 genomes]
rs7202844	0.94[EUR][1000 genomes]
rs7202858	0.93[EUR][1000 genomes]
rs7202877	0.94[EUR][1000 genomes]
rs72802372	0.94[EUR][1000 genomes]
rs72802375	0.94[EUR][1000 genomes]
rs72804106	0.89[EUR][1000 genomes]
rs73605139	0.89[EUR][1000 genomes]
rs8046145	0.89[EUR][1000 genomes]
rs8048529	0.86[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs8053595	0.94[EUR][1000 genomes]
rs8054218	0.94[EUR][1000 genomes]
rs8063014	0.89[EUR][1000 genomes]
rs9921586	0.96[EUR][1000 genomes]
rs9940370	0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:75246800-75261000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr16:75251600-75261600	Weak transcription	HMEC	breast
3	chr16:75252600-75262000	Weak transcription	Brain Angular Gyrus	brain
4	chr16:75253200-75261800	Weak transcription	Brain Anterior Caudate	brain
5	chr16:75253200-75263400	Weak transcription	HSMMtube	muscle
6	chr16:75253400-75261000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr16:75253400-75261400	Weak transcription	HSMM	muscle
8	chr16:75254000-75261400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr16:75254000-75261400	Weak transcription	NHDF-Ad	bronchial
10	chr16:75254000-75262400	Weak transcription	Brain Substantia Nigra	brain
11	chr16:75254000-75262400	Weak transcription	NH-A	brain
12	chr16:75254000-75267600	Weak transcription	Fetal Brain Male	brain
13	chr16:75254600-75268000	Weak transcription	GM12878-XiMat	blood
14	chr16:75256400-75260400	Weak transcription	Left Ventricle	heart
15	chr16:75256400-75261400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr16:75256400-75261600	Weak transcription	Aorta	Aorta
17	chr16:75256400-75266600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr16:75256600-75261000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr16:75256600-75261400	Weak transcription	Gastric	stomach
20	chr16:75256600-75262000	Weak transcription	Ovary	ovary
21	chr16:75256600-75263000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr16:75256600-75267600	Weak transcription	Fetal Heart	heart
23	chr16:75256600-75267600	Weak transcription	Right Atrium	heart
24	chr16:75257400-75261600	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr16:75257400-75261800	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr16:75257800-75260800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr16:75258200-75260600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr16:75258800-75261400	Weak transcription	Fetal Brain Female	brain
29	chr16:75258800-75262800	Weak transcription	Fetal Lung	lung
30	chr16:75259000-75262000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr16:75259000-75263200	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr16:75259200-75260600	Active TSS	Pancreas	Pancrea
33	chr16:75259200-75260800	Weak transcription	Fetal Intestine Small	intestine
34	chr16:75259200-75261000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr16:75259200-75261000	Weak transcription	Spleen	Spleen
36	chr16:75259200-75261400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr16:75259200-75261400	Weak transcription	Brain Germinal Matrix	brain
38	chr16:75259200-75261400	Weak transcription	Esophagus	oesophagus
39	chr16:75259200-75261400	Enhancers	Placenta	Placenta
40	chr16:75259200-75261600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr16:75259200-75261800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr16:75259400-75261000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr16:75259400-75261600	Weak transcription	NHEK	skin
44	chr16:75259400-75261800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr16:75259400-75267400	Weak transcription	Psoas Muscle	Psoas
46	chr16:75259600-75261000	Weak transcription	NHLF	lung
47	chr16:75259600-75261200	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr16:75259600-75261400	Weak transcription	HUVEC	blood vessel
49	chr16:75259800-75261000	Weak transcription	Brain Cingulate Gyrus	brain
50	chr16:75259800-75261400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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