Variant report

Variant	rs28566553
Chromosome Location	chr16:31085907-31085908
allele	A/G
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	PML	chr16:31083767-31086593	GM12878	blood:	n/a	n/a
2	ZNF263	chr16:31085494-31086030	K562	blood:	n/a	n/a
3	CTCF	chr16:31085840-31085990	GM12873	blood:	n/a	n/a
4	CTCF	chr16:31085880-31086030	SK-N-SH_RA	brain:	n/a	n/a
5	POLR2A	chr16:31083894-31086201	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr16:31085381-31086108	A549	lung:	n/a	n/a
7	FOSL1	chr16:31083772-31086459	HCT-116	colon:	n/a	chr16:31085077-31085086 chr16:31084994-31085004 chr16:31084994-31085004 chr16:31084844-31084853
8	RFX5	chr16:31083832-31086478	HepG2	liver:	n/a	chr16:31085735-31085749
9	POLR2A	chr16:31085318-31086345	PFSK-1	brain:	n/a	n/a
10	POLR2A	chr16:31084421-31086157	K562	blood:	n/a	n/a
11	SPI1	chr16:31085527-31086040	GM12878	blood:	n/a	chr16:31085727-31085740 chr16:31085688-31085701 chr16:31085728-31085741 chr16:31085690-31085699 chr16:31085728-31085741 chr16:31085729-31085738
12	REST	chr16:31084127-31086055	HL-60	blood:	n/a	chr16:31084730-31084743 chr16:31084772-31084792 chr16:31084936-31084949 chr16:31084847-31084865 chr16:31084772-31084792 chr16:31084939-31084952 chr16:31085665-31085678 chr16:31084772-31084792 chr16:31085754-31085772 chr16:31084773-31084791
13	TCF3	chr16:31085704-31086081	GM12878	blood:	n/a	n/a
14	ZKSCAN1	chr16:31084390-31085969	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr16:31084397-31086490	Hela-S3	cervix:	n/a	n/a
16	RELA	chr16:31084013-31086201	GM19193	blood:	n/a	n/a
17	ETS1	chr16:31085003-31085920	A549	lung:	n/a	chr16:31085633-31085644 chr16:31085073-31085084 chr16:31085633-31085642 chr16:31085547-31085556 chr16:31085543-31085559 chr16:31085076-31085087 chr16:31085631-31085640 chr16:31085547-31085556 chr16:31085110-31085119 chr16:31085547-31085556 chr16:31085633-31085642 chr16:31085092-31085105 chr16:31085671-31085684 chr16:31085547-31085558 chr16:31085075-31085086 chr16:31085547-31085556 chr16:31085547-31085556 chr16:31085728-31085737 chr16:31085633-31085642 chr16:31085725-31085738 chr16:31085633-31085642 chr16:31085633-31085642 chr16:31085111-31085121
18	TAF1	chr16:31084857-31085930	SK-N-SH	brain:	n/a	n/a
19	RAD21	chr16:31085090-31086167	HepG2	liver:	n/a	n/a
20	SIN3AK20	chr16:31085027-31085994	A549	lung:	n/a	n/a
21	POLR2A	chr16:31083730-31086483	HL-60	blood:	n/a	n/a
22	POLR2A	chr16:31085329-31086124	HUVEC	blood vessel:	n/a	n/a
23	CEBPB	chr16:31085447-31085967	ECC-1	luminal epithelium:	n/a	n/a
24	MAZ	chr16:31084415-31086100	HepG2	liver:	n/a	chr16:31084485-31084493
25	TAF1	chr16:31084904-31085952	GM12891	blood:	n/a	n/a
26	CBX3	chr16:31084346-31086000	K562	blood:	n/a	n/a
27	SIN3AK20	chr16:31084908-31086078	HepG2	liver:	n/a	n/a
28	ZNF143	chr16:31084337-31086115	GM12878	blood:	n/a	chr16:31084597-31084615 chr16:31084923-31084942
29	GABPA	chr16:31084441-31086036	GM12878	blood:	n/a	chr16:31085966-31085977 chr16:31085966-31085980 chr16:31084890-31084899 chr16:31084877-31084886 chr16:31085966-31085975 chr16:31085078-31085087 chr16:31084848-31084857 chr16:31085690-31085697 chr16:31085963-31085977
30	MXI1	chr16:31084304-31086326	HepG2	liver:	n/a	n/a
31	POLR2A	chr16:31084245-31086168	MCF-7	breast:	n/a	n/a
32	POLR2A	chr16:31085412-31086076	HepG2	liver:	n/a	n/a
33	GABPA	chr16:31085396-31085966	Hela-S3	cervix:	n/a	chr16:31085690-31085697
34	HEY1	chr16:31084332-31086306	HepG2	liver:	n/a	chr16:31084423-31084438 chr16:31084742-31084757 chr16:31084847-31084862
35	POLR2A	chr16:31083894-31086359	GM18505	blood:	n/a	n/a
36	MYC	chr16:31084479-31086046	MCF10A-Er-Src	breast:	n/a	chr16:31084485-31084493
37	E2F4	chr16:31084495-31086170	MCF10A-Er-Src	breast:	n/a	chr16:31085078-31085090 chr16:31085967-31085976 chr16:31085700-31085711 chr16:31086008-31086020 chr16:31085699-31085710 chr16:31084958-31084970 chr16:31085698-31085708 chr16:31084848-31084857 chr16:31085078-31085087 chr16:31085698-31085709 chr16:31085699-31085707 chr16:31084641-31084651 chr16:31085699-31085707
38	JUND	chr16:31084298-31086148	A549	lung:	n/a	chr16:31085077-31085086 chr16:31084994-31085004 chr16:31084994-31085004 chr16:31084844-31084853
39	EGR1	chr16:31085376-31085932	H1-hESC	embryonic stem cell:	n/a	chr16:31085592-31085606 chr16:31085595-31085604 chr16:31085728-31085737 chr16:31085594-31085604 chr16:31085593-31085604 chr16:31085592-31085605 chr16:31085633-31085642 chr16:31085588-31085610 chr16:31085593-31085604 chr16:31085593-31085607 chr16:31085660-31085673 chr16:31085594-31085604 chr16:31085547-31085556 chr16:31085592-31085605
40	POLR2A	chr16:31084345-31086443	H1-hESC	embryonic stem cell:	n/a	n/a
41	RCOR1	chr16:31084413-31085977	GM12878	blood:	n/a	n/a
42	JUN	chr16:31085499-31085910	K562	blood:	n/a	n/a
43	POLR2A	chr16:31084817-31086412	SK-N-MC	brain:	n/a	n/a
44	CHD2	chr16:31084384-31086376	GM12878	blood:	n/a	chr16:31085079-31085089
45	CTCF	chr16:31085771-31086386	IMR90	lung:	n/a	n/a
46	ELF1	chr16:31085298-31086117	HepG2	liver:	n/a	chr16:31085690-31085699 chr16:31085729-31085740 chr16:31085728-31085739 chr16:31085546-31085555
47	MBD4	chr16:31084893-31085981	HepG2	liver:	n/a	n/a
48	RELA	chr16:31084033-31086356	GM19099	blood:	n/a	n/a
49	NRF1	chr16:31085427-31086346	GM12878	blood:	n/a	chr16:31085966-31085977 chr16:31085966-31085980 chr16:31085966-31085975 chr16:31085690-31085697 chr16:31085963-31085977
50	NRF1	chr16:31085340-31086142	K562	blood:	n/a	chr16:31085966-31085977 chr16:31085966-31085980 chr16:31085966-31085975 chr16:31085690-31085697 chr16:31085963-31085977

No.	Distal block	Cell Line	Cell type
1	chr16:30993751..31000588-chr16:31082470..31087271,14	MCF-7	breast:
2	chr16:31085582..31087599-chr16:31140621..31143082,2	MCF-7	breast:
3	chr16:31083053..31086141-chr16:31468278..31470995,4	MCF-7	breast:
4	chr16:31083573..31086327-chr16:31122614..31125277,2	MCF-7	breast:
5	chr16:30967393..30971385-chr16:31083259..31086232,6	K562	blood:
6	chr16:31085525..31086089-chr3:169491238..169492056,3	Hela-S3	cervix:
7	chr16:31083048..31086004-chr16:31194000..31195518,2	K562	blood:
8	chr16:31082536..31087626-chr16:31189682..31193300,10	K562	blood:
9	chr16:30932689..30934576-chr16:31084033..31085909,2	MCF-7	breast:
10	chr16:31083418..31087298-chr16:31127627..31129856,4	MCF-7	breast:
11	chr12:80084777..80085326-chr16:31085636..31086179,2	Hela-S3	cervix:
12	chr16:31082772..31088721-chr16:31466605..31471958,8	MCF-7	breast:
13	chr16:30967179..30972282-chr16:31082507..31088894,13	MCF-7	breast:
14	chr16:31083571..31086239-chr16:31118530..31123064,5	MCF-7	breast:
15	chr16:31085251..31088144-chr16:31197291..31199789,2	MCF-7	breast:
16	chr16:31083121..31087142-chr16:31201423..31205329,4	K562	blood:
17	chr16:31043716..31047464-chr16:31083118..31086519,10	MCF-7	breast:
18	chr16:31082869..31088846-chr16:31189629..31192848,9	MCF-7	breast:
19	chr16:31082745..31087235-chr16:31149717..31155170,6	K562	blood:
20	chr16:31006807..31011358-chr16:31082999..31086095,12	MCF-7	breast:
21	chr16:30967600..30970776-chr16:31084507..31087266,4	MCF-7	breast:
22	chr16:31085806..31086478-chr2:176987025..176987881,2	Hela-S3	cervix:
23	chr16:31043013..31046253-chr16:31082389..31087326,7	K562	blood:
24	chr16:31083033..31088054-chr16:31143674..31155673,17	MCF-7	breast:
25	chr16:31076302..31081402-chr16:31082512..31087316,9	K562	blood:
26	chr16:31085473..31086240-chr3:57261347..57261934,2	Hela-S3	cervix:
27	chr16:31043013..31047219-chr16:31082783..31087326,13	K562	blood:
28	chr16:31084212..31086382-chr16:31118397..31120313,2	K562	blood:
29	chr16:31083902..31086771-chr16:31468748..31470468,2	K562	blood:
30	chr16:31082041..31086874-chr16:31152182..31155388,6	MCF-7	breast:
31	chr16:31083950..31086664-chr16:31145533..31147488,3	MCF-7	breast:
32	chr16:31084138..31086184-chr16:31153280..31154871,2	K562	blood:
33	chr16:31083069..31087057-chr16:31126898..31130730,7	K562	blood:
34	chr16:30959935..30962843-chr16:31083365..31086256,4	MCF-7	breast:
35	chr16:31084135..31087518-chr16:31711748..31714825,3	MCF-7	breast:
36	chr16:31043007..31053782-chr16:31072765..31087431,40	MCF-7	breast:
37	chr16:30709031..30710824-chr16:31084721..31086312,2	MCF-7	breast:
38	chr16:31007911..31010328-chr16:31084206..31087011,2	K562	blood:
39	chr16:31084383..31087189-chr16:31118914..31120512,2	MCF-7	breast:
40	chr16:31084249..31087581-chr16:31125866..31130783,7	MCF-7	breast:
41	chr16:31083873..31090665-chr16:31187351..31192875,15	MCF-7	breast:
42	chr16:31082583..31087626-chr16:31190328..31193369,8	K562	blood:
43	chr16:30991043..31010547-chr16:31082350..31088728,42	MCF-7	breast:
44	chr16:30967393..30971949-chr16:31083830..31088417,7	K562	blood:
45	chr16:31083576..31088702-chr16:31125774..31130494,10	K562	blood:

Variant related genes	Relation type
ZNF668	TF binding region
ZNF646	TF binding region
ENSG00000099365	Chromatin interaction
ENSG00000262766	Chromatin interaction
ENSG00000167394	Chromatin interaction
ENSG00000099377	Chromatin interaction
ENSG00000261840	Chromatin interaction
ENSG00000052344	Chromatin interaction
ENSG00000131797	Chromatin interaction
ENSG00000261124	Chromatin interaction
ENSG00000103510	Chromatin interaction
ENSG00000178226	Chromatin interaction
ENSG00000260267	Chromatin interaction
ENSG00000103496	Chromatin interaction
ENSG00000252809	Chromatin interaction
ENSG00000099381	Chromatin interaction
ENSG00000080603	Chromatin interaction
ENSG00000085274	Chromatin interaction
ENSG00000157500	Chromatin interaction
ENSG00000261385	Chromatin interaction
ENSG00000175938	Chromatin interaction
ENSG00000177425	Chromatin interaction
ENSG00000140691	Chromatin interaction
ENSG00000260568	Chromatin interaction
ENSG00000099364	Chromatin interaction
ENSG00000103507	Chromatin interaction
ENSG00000128709	Chromatin interaction
ENSG00000268863	Chromatin interaction
ENSG00000089280	Chromatin interaction
ENSG00000260304	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs13337470	1.00[AFR][1000 genomes]
rs59532700	0.82[AFR][1000 genomes]
rs8053474	1.00[AFR][1000 genomes]
rs9889109	0.82[AFR][1000 genomes]
rs9924048	0.84[AFR][1000 genomes]
rs9924515	0.82[AFR][1000 genomes]
rs9925820	0.82[AFR][1000 genomes]
rs9932671	0.82[AFR][1000 genomes]

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	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	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
6	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
7	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
8	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
9	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
10	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
11	nsv833193	chr16:30960796-31133604	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription 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	109 gene(s)	inside rSNPs	diseases
12	nsv905740	chr16:31066249-31232437	Flanking Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	202 gene(s)	inside rSNPs	diseases
13	nsv905741	chr16:31066249-31247924	Genic enhancers Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	202 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:31083200-31086600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr16:31083200-31086600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr16:31083200-31086800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr16:31083600-31086200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr16:31083600-31086600	Active TSS	H9 Cell Line	embryonic stem cell
6	chr16:31083600-31086800	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr16:31083600-31086800	Active TSS	GM12878-XiMat	blood
8	chr16:31083800-31086200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr16:31083800-31086200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr16:31083800-31086200	Active TSS	Brain Germinal Matrix	brain
11	chr16:31083800-31086200	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr16:31083800-31086400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
13	chr16:31083800-31086400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr16:31083800-31086400	Active TSS	iPS-15b Cell Line	embryonic stem cell
15	chr16:31083800-31086400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr16:31083800-31086400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr16:31083800-31086400	Active TSS	Fetal Brain Male	brain
18	chr16:31083800-31086400	Bivalent/Poised TSS	HepG2	liver
19	chr16:31083800-31086600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr16:31083800-31086600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr16:31083800-31086600	Active TSS	A549	lung
22	chr16:31083800-31086600	Active TSS	HSMMtube	muscle
23	chr16:31083800-31086600	Active TSS	NHLF	lung
24	chr16:31083800-31086800	Active TSS	HUES48 Cell Line	embryonic stem cell
25	chr16:31083800-31086800	Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr16:31084000-31086000	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr16:31084000-31086200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
28	chr16:31084000-31086200	Active TSS	Primary T killer memory cells from peripheral blood	blood
29	chr16:31084000-31086200	Active TSS	Muscle Satellite Cultured Cells	--
30	chr16:31084000-31086200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr16:31084000-31086200	Active TSS	Fetal Brain Female	brain
32	chr16:31084000-31086200	Active TSS	Gastric	stomach
33	chr16:31084000-31086200	Active TSS	Dnd41	blood
34	chr16:31084000-31086200	Active TSS	Hela-S3	cervix
35	chr16:31084000-31086200	Active TSS	HMEC	breast
36	chr16:31084000-31086200	Active TSS	HUVEC	blood vessel
37	chr16:31084000-31086200	Active TSS	NH-A	brain
38	chr16:31084000-31086400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr16:31084000-31086400	Active TSS	Fetal Kidney	kidney
40	chr16:31084000-31086400	Active TSS	Ovary	ovary
41	chr16:31084000-31086400	Active TSS	Placenta Amnion	Placenta Amnion
42	chr16:31084000-31086400	Active TSS	Sigmoid Colon	Sigmoid Colon
43	chr16:31084000-31086400	Active TSS	Small Intestine	intestine
44	chr16:31084000-31086400	Active TSS	HSMM	muscle
45	chr16:31084000-31086400	Active TSS	K562	blood
46	chr16:31084000-31086400	Active TSS	NHEK	skin
47	chr16:31084000-31086600	Active TSS	ES-I3 Cell Line	embryonic stem cell
48	chr16:31084000-31086600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr16:31084000-31086600	Active TSS	iPS-18 Cell Line	embryonic stem cell
50	chr16:31084000-31086600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell

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