Variant report

Variant	rs16873361
Chromosome Location	chr5:43483378-43483379
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:233)
CpG islands
(count:0)
Chromatin interactive
region (count:52)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:233 , 50 per page) page: 1 2 3 4 5

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr5:43482536-43485365	SK-N-SH	brain:	n/a	n/a
2	CBX3	chr5:43483306-43484842	K562	blood:	n/a	n/a
3	CEBPB	chr5:43482974-43484235	K562	blood:	n/a	chr5:43483423-43483434
4	YY1	chr5:43483355-43484643	HepG2	liver:	n/a	chr5:43483670-43483684
5	TAF1	chr5:43483305-43484625	A549	lung:	n/a	n/a
6	TAF1	chr5:43483347-43483541	SK-N-SH	brain:	n/a	n/a
7	HDAC2	chr5:43483377-43484194	HepG2	liver:	n/a	n/a
8	RUNX3	chr5:43483305-43484916	GM12878	blood:	n/a	chr5:43484014-43484029
9	TAF1	chr5:43483321-43484605	Hela-S3	cervix:	n/a	n/a
10	MYC	chr5:43483286-43484839	K562	blood:	n/a	chr5:43483760-43483769
11	SIN3AK20	chr5:43483374-43483664	H1-hESC	embryonic stem cell:	n/a	n/a
12	MXI1	chr5:43483375-43484863	GM12878	blood:	n/a	n/a
13	JUND	chr5:43482529-43483736	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr5:43483214-43484898	GM18505	blood:	n/a	n/a
15	TBP	chr5:43483313-43484827	K562	blood:	n/a	n/a
16	POLR2A	chr5:43483286-43484950	U87	brain:	n/a	n/a
17	MAX	chr5:43483260-43484811	HepG2	liver:	n/a	chr5:43483760-43483769
18	YY1	chr5:43483307-43484631	GM12878	blood:	n/a	chr5:43483670-43483684
19	POLR2A	chr5:43483307-43484916	K562	blood:	n/a	n/a
20	PML	chr5:43483348-43483622	GM12878	blood:	n/a	n/a
21	BRCA1	chr5:43482529-43485182	Hela-S3	cervix:	n/a	n/a
22	ATF2	chr5:43483196-43484812	GM12878	blood:	n/a	n/a
23	POLR2A	chr5:43483230-43485020	MCF-7	breast:	n/a	n/a
24	STAT3	chr5:43483280-43483480	MCF10A-Er-Src	breast:	n/a	n/a
25	CEBPB	chr5:43483235-43483642	ECC-1	luminal epithelium:	n/a	chr5:43483423-43483434
26	FOS	chr5:43482655-43483447	MCF10A-Er-Src	breast:	n/a	n/a
27	IRF1	chr5:43483269-43484931	K562	blood:	n/a	chr5:43484835-43484845 chr5:43484833-43484853 chr5:43484153-43484166 chr5:43483354-43483370 chr5:43483289-43483296 chr5:43484831-43484848 chr5:43484152-43484166
28	TAL1	chr5:43482794-43484763	K562	blood:	n/a	n/a
29	POLR2A	chr5:43483237-43484873	PBDE	blood:	n/a	n/a
30	MYBL2	chr5:43483316-43484576	HepG2	liver:	n/a	n/a
31	MAX	chr5:43483254-43484987	A549	lung:	n/a	chr5:43483760-43483769
32	JUND	chr5:43483278-43483594	HepG2	liver:	n/a	n/a
33	POLR2A	chr5:43482241-43485297	K562	blood:	n/a	n/a
34	POLR2A	chr5:43483327-43484899	IMR90	lung:	n/a	n/a
35	ZNF143	chr5:43483374-43484731	GM12878	blood:	n/a	n/a
36	POLR2A	chr5:43482641-43485033	PFSK-1	brain:	n/a	n/a
37	POLR2A	chr5:43483373-43484573	HUVEC	blood vessel:	n/a	n/a
38	TAF1	chr5:43483373-43484731	K562	blood:	n/a	n/a
39	RELA	chr5:43483298-43484764	GM15510	blood:	n/a	n/a
40	REST	chr5:43483296-43484666	HL-60	blood:	n/a	chr5:43483688-43483701
41	MAX	chr5:43483260-43484913	NB4	blood:	n/a	chr5:43483760-43483769
42	MXI1	chr5:43482507-43485320	IMR90	lung:	n/a	n/a
43	CEBPB	chr5:43483184-43483615	A549	lung:	n/a	chr5:43483423-43483434
44	POLR2A	chr5:43483309-43484923	GM12891	blood:	n/a	n/a
45	BHLHE40	chr5:43483368-43484918	K562	blood:	n/a	n/a
46	PML	chr5:43483208-43484885	K562	blood:	n/a	n/a
47	POLR2A	chr5:43483121-43484998	H1-hESC	embryonic stem cell:	n/a	n/a
48	TCF7L2	chr5:43483317-43484784	Hela-S3	cervix:	n/a	n/a
49	POLR2A	chr5:43483275-43484867	GM12891	blood:	n/a	n/a
50	NR2F2	chr5:43483333-43483767	K562	blood:	n/a	n/a

No data

(count:52 , 50 per page) page: 1 2

No.	Distal block	Cell Line	Cell type
1	chr5:43192100..43194083-chr5:43481713..43484639,2	MCF-7	breast:
2	chr1:174967977..174968624-chr5:43483323..43483996,2	Hela-S3	cervix:
3	chr5:43120765..43125898-chr5:43482451..43485837,5	K562	blood:
4	chr5:43064858..43068068-chr5:43482667..43486392,7	K562	blood:
5	chr5:43481238..43485996-chr5:43553681..43560344,12	K562	blood:
6	chr5:43481891..43486310-chr5:43553986..43559337,13	K562	blood:
7	chr5:43311997..43315552-chr5:43481611..43486076,8	MCF-7	breast:
8	chr5:43482505..43485566-chr5:43554663..43558409,7	MCF-7	breast:
9	chr5:43064382..43066342-chr5:43482298..43484520,2	MCF-7	breast:
10	chr5:43482483..43486113-chr5:43601084..43606081,7	K562	blood:
11	chr5:43073690..43076137-chr5:43481731..43483663,2	MCF-7	breast:
12	chr5:43394691..43398587-chr5:43480937..43485812,7	MCF-7	breast:
13	chr5:43483154..43484026-chr5:150460085..150460932,2	Hela-S3	cervix:
14	chr12:107349557..107350126-chr5:43483366..43484255,2	Hela-S3	cervix:
15	chr5:43482302..43485563-chr5:43510151..43513746,5	MCF-7	breast:
16	chr5:43395776..43403836-chr5:43482661..43487155,15	MCF-7	breast:
17	chr5:43119575..43121406-chr5:43482478..43484102,2	MCF-7	breast:
18	chr5:43481246..43484731-chr5:43603166..43606245,4	K562	blood:
19	chr1:17222217..17222917-chr5:43483114..43484118,3	Hela-S3	cervix:
20	chr5:43065608..43069318-chr5:43481836..43485606,6	MCF-7	breast:
21	chr5:43062770..43067811-chr5:43482181..43486392,9	K562	blood:
22	chr5:43006524..43009170-chr5:43481827..43484461,4	K562	blood:
23	chr16:30645535..30646046-chr5:43483024..43483856,2	Hela-S3	cervix:
24	chr5:43481800..43486706-chr5:43511486..43517226,18	K562	blood:
25	chr5:43481776..43485753-chr5:43513662..43518339,9	MCF-7	breast:
26	chr5:43006142..43009170-chr5:43482864..43485007,3	K562	blood:
27	chr5:43483317..43484109-chr8:120219923..120220769,2	Hela-S3	cervix:
28	chr16:30709290..30710319-chr5:43483061..43484030,3	Hela-S3	cervix:
29	chr11:3013443..3014405-chr5:43483115..43483926,2	Hela-S3	cervix:
30	chr5:43410322..43414589-chr5:43481701..43485572,7	K562	blood:
31	chr5:43452221..43453940-chr5:43481529..43483872,2	K562	blood:
32	chr19:49121990..49122525-chr5:43483356..43484094,2	Hela-S3	cervix:
33	chr14:58764430..58765011-chr5:43483076..43483736,2	Hela-S3	cervix:
34	chr11:57435390..57435953-chr5:43483041..43483860,2	Hela-S3	cervix:
35	chr14:24740301..24740877-chr5:43483323..43484152,2	Hela-S3	cervix:
36	chr5:43408350..43414682-chr5:43482713..43485961,9	MCF-7	breast:
37	chr5:43119639..43122584-chr5:43481498..43484654,4	K562	blood:
38	chr5:43482757..43485165-chr5:43504777..43508621,4	MCF-7	breast:
39	chr5:43458177..43460519-chr5:43482121..43483647,2	K562	blood:
40	chr5:43482545..43485280-chr5:43513880..43516299,2	MCF-7	breast:
41	chr5:43040725..43043389-chr5:43482013..43483748,2	MCF-7	breast:
42	chr3:99536369..99537348-chr5:43483024..43483929,2	Hela-S3	cervix:
43	chr5:43482042..43485833-chr5:43601604..43604541,3	MCF-7	breast:
44	chr5:43479992..43486255-chr5:43553479..43560182,13	MCF-7	breast:
45	chr5:43483358..43483893-chr6:170124844..170125678,2	Hela-S3	cervix:
46	chr5:43482660..43486669-chr5:43512252..43517355,11	K562	blood:
47	chr5:43483341..43484055-chr9:139257330..139258217,2	Hela-S3	cervix:
48	chr5:43410262..43414589-chr5:43481541..43486559,6	K562	blood:
49	chr5:43482924..43484837-chr5:43505826..43508408,3	MCF-7	breast:
50	chr20:30192739..30193386-chr5:43483323..43484505,3	Hela-S3	cervix:

No data

Variant related genes	Relation type
ENSG00000249492	TF binding region
ENSG00000063177	Chromatin interaction
ENSG00000177453	Chromatin interaction
ENSG00000184220	Chromatin interaction
ENSG00000248554	Chromatin interaction
ENSG00000248240	Chromatin interaction
ENSG00000147676	Chromatin interaction
ENSG00000139971	Chromatin interaction
ENSG00000112992	Chromatin interaction
ENSG00000248092	Chromatin interaction
ENSG00000205531	Chromatin interaction
ENSG00000207005	Chromatin interaction
ENSG00000151882	Chromatin interaction
ENSG00000177738	Chromatin interaction
ENSG00000112972	Chromatin interaction
ENSG00000213221	Chromatin interaction
ENSG00000145901	Chromatin interaction
ENSG00000261840	Chromatin interaction
ENSG00000172239	Chromatin interaction
ENSG00000271788	Chromatin interaction
ENSG00000177721	Chromatin interaction
ENSG00000227704	Chromatin interaction
ENSG00000159216	Chromatin interaction
ENSG00000100949	Chromatin interaction
ENSG00000257621	Chromatin interaction
ENSG00000172244	Chromatin interaction
ENSG00000116161	Chromatin interaction
ENSG00000156599	Chromatin interaction
ENSG00000151135	Chromatin interaction
ENSG00000125968	Chromatin interaction
ENSG00000172262	Chromatin interaction
ENSG00000080603	Chromatin interaction
ENSG00000215068	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs16873327	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6867927	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6880159	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6884864	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6885326	0.85[EUR][1000 genomes]
rs6886244	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6896589	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6897816	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7716564	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7728139	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881017	chr5:43444826-43731692	Weak transcription Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	222 gene(s)	inside rSNPs	diseases
2	nsv830275	chr5:43469511-43639384	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	220 gene(s)	inside rSNPs	diseases
3	esv1802134	chr5:43476545-43492449	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	142 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16873361	NNT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43433800-43483400	Weak transcription	Gastric	stomach
2	chr5:43461200-43483400	Weak transcription	Pancreas	Pancrea
3	chr5:43462400-43483400	Weak transcription	Spleen	Spleen
4	chr5:43468800-43483400	Weak transcription	Ovary	ovary
5	chr5:43470600-43483400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr5:43472200-43483400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr5:43474000-43483400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr5:43476600-43483400	Weak transcription	Lung	lung
9	chr5:43482200-43484600	Active TSS	HSMMtube	muscle
10	chr5:43482400-43484600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr5:43482400-43484600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr5:43482400-43484600	Active TSS	A549	lung
13	chr5:43482400-43484600	Active TSS	GM12878-XiMat	blood
14	chr5:43482400-43484600	Active TSS	K562	blood
15	chr5:43482400-43484600	Active TSS	NHLF	lung
16	chr5:43482600-43483400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr5:43482600-43483400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr5:43482600-43483400	Flanking Active TSS	Hela-S3	cervix
19	chr5:43482600-43483600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
20	chr5:43482600-43484600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr5:43482600-43484600	Active TSS	HMEC	breast
22	chr5:43482600-43484600	Active TSS	NHDF-Ad	bronchial
23	chr5:43482600-43484600	Active TSS	NHEK	skin
24	chr5:43482600-43484800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
25	chr5:43482600-43484800	Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr5:43482600-43485200	Active TSS	iPS-20b Cell Line	embryonic stem cell
27	chr5:43482800-43483400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
28	chr5:43482800-43483400	Flanking Active TSS	Duodenum Mucosa	Duodenum
29	chr5:43482800-43483400	Flanking Active TSS	Fetal Kidney	kidney
30	chr5:43482800-43483400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
31	chr5:43482800-43483400	Enhancers	Small Intestine	intestine
32	chr5:43482800-43483400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
33	chr5:43482800-43483600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr5:43482800-43483800	Active TSS	Right Atrium	heart
35	chr5:43482800-43483800	Flanking Active TSS	Stomach Smooth Muscle	stomach
36	chr5:43482800-43484600	Active TSS	ES-I3 Cell Line	embryonic stem cell
37	chr5:43482800-43484600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr5:43482800-43484600	Active TSS	iPS-15b Cell Line	embryonic stem cell
39	chr5:43482800-43484600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr5:43482800-43484600	Active TSS	Muscle Satellite Cultured Cells	--
41	chr5:43482800-43484600	Active TSS	Fetal Muscle Leg	muscle
42	chr5:43482800-43484800	Active TSS	H1 Cell Line	embryonic stem cell
43	chr5:43482800-43484800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr5:43482800-43484800	Active TSS	Pancreatic Islets	Pancreatic Islet
45	chr5:43482800-43484800	Active TSS	Right Ventricle	heart
46	chr5:43482800-43485000	Active TSS	HUES48 Cell Line	embryonic stem cell
47	chr5:43482800-43485000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr5:43483000-43483400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
49	chr5:43483000-43483400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
50	chr5:43483000-43483400	Flanking Active TSS	Adipose Nuclei	Adipose

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