Variant report

Variant	rs56314408
Chromosome Location	chr16:31117389-31117390
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	SP1	chr16:31117024-31117517	HepG2	liver:	n/a	chr16:31117487-31117494
2	MAX	chr16:31117046-31117530	ECC-1	luminal epithelium:	n/a	chr16:31117262-31117271 chr16:31117261-31117272
3	TAL1	chr16:31117108-31117401	K562	blood:	n/a	n/a
4	POLR2A	chr16:31117110-31117484	HepG2	liver:	n/a	n/a
5	ZKSCAN1	chr16:31117117-31117459	Hela-S3	cervix:	n/a	n/a
6	BHLHE40	chr16:31117045-31117426	GM12878	blood:	n/a	chr16:31117125-31117141
7	MYC	chr16:31117056-31117552	MCF-7	breast:	n/a	chr16:31117262-31117271 chr16:31117261-31117272
8	MAX	chr16:31117056-31117470	Hela-S3	cervix:	n/a	chr16:31117262-31117271 chr16:31117261-31117272
9	ATF3	chr16:31117023-31117527	HepG2	liver:	n/a	n/a
10	JUN	chr16:31117041-31117546	K562	blood:	n/a	n/a
11	MAX	chr16:31117028-31117503	K562	blood:	n/a	chr16:31117262-31117271 chr16:31117261-31117272
12	POLR2A	chr16:31117070-31117550	HepG2	liver:	n/a	n/a
13	HEY1	chr16:31117107-31117462	HepG2	liver:	n/a	n/a
14	MYC	chr16:31117017-31117457	Hela-S3	cervix:	n/a	chr16:31117262-31117271 chr16:31117261-31117272
15	MAX	chr16:31117044-31117515	H1-hESC	embryonic stem cell:	n/a	chr16:31117262-31117271 chr16:31117261-31117272
16	RAD21	chr16:31116967-31117407	H1-hESC	embryonic stem cell:	n/a	chr16:31117126-31117139
17	RAD21	chr16:31117018-31117391	MCF-7	breast:	n/a	chr16:31117126-31117139
18	YY1	chr16:31117039-31117454	K562	blood:	n/a	chr16:31117255-31117264
19	MYC	chr16:31117042-31117475	K562	blood:	n/a	chr16:31117262-31117271 chr16:31117261-31117272
20	CTCF	chr16:31116959-31117405	K562	blood:	n/a	chr16:31117126-31117139
21	E2F6	chr16:31117074-31117482	K562	blood:	n/a	chr16:31117346-31117358 chr16:31117129-31117139 chr16:31117393-31117403
22	MAX	chr16:31117045-31117622	HepG2	liver:	n/a	chr16:31117262-31117271 chr16:31117261-31117272
23	ELK1	chr16:31117184-31117390	K562	blood:	n/a	n/a
24	RAD21	chr16:31117016-31117464	ECC-1	luminal epithelium:	n/a	chr16:31117126-31117139
25	FOSL2	chr16:31116934-31117459	HepG2	liver:	n/a	n/a
26	ZNF384	chr16:31116950-31117414	K562	blood:	n/a	n/a
27	CEBPB	chr16:31117221-31117551	A549	lung:	n/a	n/a
28	E2F6	chr16:31117035-31117500	K562	blood:	n/a	chr16:31117346-31117358 chr16:31117129-31117139 chr16:31117393-31117403
29	MAX	chr16:31117034-31117549	K562	blood:	n/a	chr16:31117262-31117271 chr16:31117261-31117272
30	RAD21	chr16:31117032-31117435	A549	lung:	n/a	chr16:31117126-31117139
31	E2F6	chr16:31117076-31117532	A549	lung:	n/a	chr16:31117346-31117358 chr16:31117129-31117139 chr16:31117393-31117403
32	RAD21	chr16:31117039-31117525	HCT-116	colon:	n/a	chr16:31117126-31117139
33	MAX	chr16:31116999-31117491	NB4	blood:	n/a	chr16:31117262-31117271 chr16:31117261-31117272
34	TBP	chr16:31117085-31117416	HepG2	liver:	n/a	n/a
35	EP300	chr16:31116974-31117583	HepG2	liver:	n/a	chr16:31117123-31117139 chr16:31117125-31117141 chr16:31117126-31117142
36	TCF12	chr16:31117017-31117493	HepG2	liver:	n/a	chr16:31117132-31117142
37	ZNF263	chr16:31117095-31117496	HEK293-T-REx	kidney:	n/a	n/a
38	NFIC	chr16:31117028-31117637	HepG2	liver:	n/a	n/a
39	RAD21	chr16:31116995-31117402	MCF-7	breast:	n/a	chr16:31117126-31117139
40	HDAC2	chr16:31117022-31117555	HepG2	liver:	n/a	n/a
41	EP300	chr16:31117031-31117429	SK-N-SH_RA	brain:	n/a	chr16:31117123-31117139 chr16:31117125-31117141 chr16:31117126-31117142
42	CHD2	chr16:31117109-31117505	HepG2	liver:	n/a	n/a
43	MYBL2	chr16:31116914-31117629	HepG2	liver:	n/a	n/a
44	MYC	chr16:31116963-31117557	K562	blood:	n/a	chr16:31117262-31117271 chr16:31117261-31117272
45	MYC	chr16:31116996-31117498	K562	blood:	n/a	chr16:31117262-31117271 chr16:31117261-31117272
46	USF1	chr16:31117031-31117434	A549	lung:	n/a	chr16:31117125-31117141 chr16:31117260-31117271
47	MAX	chr16:31117057-31117504	SK-N-SH	brain:	n/a	chr16:31117262-31117271 chr16:31117261-31117272
48	YY1	chr16:31117055-31117417	K562	blood:	n/a	chr16:31117255-31117264
49	POLR2A	chr16:31117025-31117469	GM12892	blood:	n/a	n/a
50	POLR2A	chr16:31117054-31117555	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:31115598..31118169-chr16:31120150..31122491,2	K562	blood:
2	chr16:30960093..30962910-chr16:31117078..31118783,2	K562	blood:
3	chr16:31116671..31117702-chr16:31153398..31154356,8	MCF-7	breast:
4	chr16:31115614..31117488-chr16:31191253..31194151,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000252809	TF binding region
BCKDK	TF binding region
ENSG00000178226	Chromatin interaction
ENSG00000103507	Chromatin interaction
ENSG00000175938	Chromatin interaction
ENSG00000252809	Chromatin interaction
ENSG00000089280	Chromatin interaction

Extended variants
information (count: 101 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs1060506	1.00[ASN][1000 genomes]
rs10871454	0.80[ASN][1000 genomes]
rs1108431	0.84[ASN][1000 genomes]
rs11150604	0.84[ASN][1000 genomes]
rs11640767	0.82[ASN][1000 genomes]
rs11640957	0.82[ASN][1000 genomes]
rs11642192	0.93[ASN][1000 genomes]
rs11647284	0.95[ASN][1000 genomes]
rs11647442	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11862744	0.84[ASN][1000 genomes]
rs11864806	0.95[ASN][1000 genomes]
rs11864839	0.95[ASN][1000 genomes]
rs11865038	0.95[ASN][1000 genomes]
rs11865499	1.00[ASN][1000 genomes]
rs12445650	0.84[ASN][1000 genomes]
rs12448321	0.84[ASN][1000 genomes]
rs12597511	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12716981	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12716982	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12934418	0.84[ASN][1000 genomes]
rs14235	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1549293	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17839567	0.84[ASN][1000 genomes]
rs17839568	0.95[ASN][1000 genomes]
rs1978485	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1978487	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2032915	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2288004	0.84[ASN][1000 genomes]
rs2303222	0.95[ASN][1000 genomes]
rs2303223	0.93[ASN][1000 genomes]
rs2359612	0.95[ASN][1000 genomes]
rs2855475	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28725459	0.96[ASN][1000 genomes]
rs28814987	0.95[ASN][1000 genomes]
rs2884738	1.00[ASN][1000 genomes]
rs34649473	0.81[ASN][1000 genomes]
rs35351013	0.89[ASN][1000 genomes]
rs35468353	0.84[ASN][1000 genomes]
rs35713203	0.95[ASN][1000 genomes]
rs3751855	0.95[ASN][1000 genomes]
rs4468641	0.95[ASN][1000 genomes]
rs4527034	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4889530	0.82[ASN][1000 genomes]
rs4889619	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4889620	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55766044	1.00[ASN][1000 genomes]
rs55979739	0.84[ASN][1000 genomes]
rs56284083	0.84[ASN][1000 genomes]
rs56813533	0.89[ASN][1000 genomes]
rs57434408	0.86[ASN][1000 genomes]
rs58726213	0.82[ASN][1000 genomes]
rs59061704	0.82[ASN][1000 genomes]
rs59735493	1.00[ASN][1000 genomes]
rs60996860	0.96[ASN][1000 genomes]
rs61162043	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61320757	1.00[ASN][1000 genomes]
rs6565217	0.95[ASN][1000 genomes]
rs7187995	0.89[ASN][1000 genomes]
rs7196161	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7196726	0.95[ASN][1000 genomes]
rs7197717	0.95[ASN][1000 genomes]
rs7199949	0.95[ASN][1000 genomes]
rs7294	0.95[ASN][1000 genomes]
rs732172	0.84[ASN][1000 genomes]
rs732173	0.84[ASN][1000 genomes]
rs73530203	0.93[ASN][1000 genomes]
rs749670	0.95[ASN][1000 genomes]
rs749671	0.95[ASN][1000 genomes]
rs749767	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7500176	0.84[ASN][1000 genomes]
rs750952	0.95[ASN][1000 genomes]
rs8047803	0.95[ASN][1000 genomes]
rs8050894	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8056842	0.84[ASN][1000 genomes]
rs8061047	0.89[ASN][1000 genomes]
rs881929	0.95[ASN][1000 genomes]
rs889548	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs889555	1.00[ASN][1000 genomes]
rs9923231	0.95[ASN][1000 genomes]
rs9925964	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9929899	0.82[ASN][1000 genomes]
rs9934438	0.95[ASN][1000 genomes]
rs9936329	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9939417	0.84[ASN][1000 genomes]
rs9939558	0.84[ASN][1000 genomes]
rs9972727	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	nsv905742	chr16:31102321-31247924	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	188 gene(s)	inside rSNPs	diseases
14	nsv905743	chr16:31111064-31129942	Genic enhancers Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription 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	35 gene(s)	inside rSNPs	diseases
15	esv3377881	chr16:31114651-31117399	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs56314408	KAT8	cis	Skin Sun Exposed Lower leg	GTEx
rs56314408	RP11-196G11.2	cis	Muscle Skeletal	GTEx
rs56314408	HSD3B7	cis	Whole Blood	GTEx
rs56314408	KAT8	cis	Artery Tibial	GTEx

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:31112800-31119200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr16:31113000-31119400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr16:31114600-31119400	Weak transcription	Lung	lung
4	chr16:31116400-31119000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr16:31117000-31117400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr16:31117000-31117400	Enhancers	Placenta Amnion	Placenta Amnion
7	chr16:31117000-31117400	Enhancers	HMEC	breast
8	chr16:31117000-31117400	Flanking Active TSS	K562	blood
9	chr16:31117000-31117600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr16:31117000-31117600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr16:31117000-31117600	Enhancers	Primary B cells from peripheral blood	blood
12	chr16:31117000-31117600	Enhancers	Primary T cells fromperipheralblood	blood
13	chr16:31117000-31117600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr16:31117000-31117600	Enhancers	Fetal Muscle Trunk	muscle
15	chr16:31117000-31117600	Enhancers	Placenta	Placenta
16	chr16:31117200-31117400	Enhancers	H1 Cell Line	embryonic stem cell
17	chr16:31117200-31117400	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr16:31117200-31117400	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr16:31117200-31117400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
20	chr16:31117200-31117400	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr16:31117200-31117400	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
22	chr16:31117200-31117400	Enhancers	Primary B cells from cord blood	blood
23	chr16:31117200-31117400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr16:31117200-31117400	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr16:31117200-31117400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr16:31117200-31117400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
27	chr16:31117200-31117400	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr16:31117200-31117400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
29	chr16:31117200-31117400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr16:31117200-31117400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr16:31117200-31117400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr16:31117200-31117400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
33	chr16:31117200-31117400	Enhancers	Aorta	Aorta
34	chr16:31117200-31117400	Flanking Active TSS	Brain Angular Gyrus	brain
35	chr16:31117200-31117400	Enhancers	Brain Cingulate Gyrus	brain
36	chr16:31117200-31117400	Enhancers	Brain Hippocampus Middle	brain
37	chr16:31117200-31117400	Enhancers	Brain Inferior Temporal Lobe	brain
38	chr16:31117200-31117400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
39	chr16:31117200-31117400	Enhancers	Brain Substantia Nigra	brain
40	chr16:31117200-31117400	Enhancers	Colon Smooth Muscle	Colon
41	chr16:31117200-31117400	Enhancers	Duodenum Mucosa	Duodenum
42	chr16:31117200-31117400	Enhancers	Esophagus	oesophagus
43	chr16:31117200-31117400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
44	chr16:31117200-31117400	Enhancers	Fetal Brain Male	brain
45	chr16:31117200-31117400	Enhancers	Fetal Heart	heart
46	chr16:31117200-31117400	Enhancers	Fetal Stomach	stomach
47	chr16:31117200-31117400	Enhancers	Gastric	stomach
48	chr16:31117200-31117400	Enhancers	Left Ventricle	heart
49	chr16:31117200-31117400	Enhancers	Ovary	ovary
50	chr16:31117200-31117400	Enhancers	Psoas Muscle	Psoas

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