Variant report

Variant	rs12923990
Chromosome Location	chr16:71757395-71757396
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	MAZ	chr16:71756616-71758293	GM12878	blood:	n/a	chr16:71757985-71757994 chr16:71757398-71757407
2	TAF1	chr16:71756752-71758033	ECC-1	luminal epithelium:	n/a	n/a
3	EGR1	chr16:71757184-71757805	K562	blood:	n/a	chr16:71757575-71757584 chr16:71757575-71757585 chr16:71757572-71757585 chr16:71757474-71757484 chr16:71757572-71757585 chr16:71757572-71757585
4	POLR2A	chr16:71756829-71758129	ProgFib	skin:	n/a	n/a
5	TAF1	chr16:71756754-71758163	H1-hESC	embryonic stem cell:	n/a	n/a
6	EGR1	chr16:71757265-71757773	GM12878	blood:	n/a	chr16:71757575-71757584 chr16:71757575-71757585 chr16:71757572-71757585 chr16:71757474-71757484 chr16:71757572-71757585 chr16:71757572-71757585
7	POLR2A	chr16:71756749-71758263	H1-neurons	neurons:	n/a	n/a
8	E2F6	chr16:71756996-71758318	K562	blood:	n/a	chr16:71757575-71757585 chr16:71757417-71757426 chr16:71758032-71758041 chr16:71757578-71757588 chr16:71757474-71757483 chr16:71757190-71757199 chr16:71758084-71758096 chr16:71757826-71757835 chr16:71757183-71757193
9	POLR2A	chr16:71756799-71758243	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr16:71756716-71758390	H1-hESC	embryonic stem cell:	n/a	n/a
11	TCF12	chr16:71756783-71757429	ECC-1	luminal epithelium:	n/a	n/a
12	POLR2A	chr16:71756800-71758261	GM12892	blood:	n/a	n/a
13	MAX	chr16:71757375-71758280	GM12878	blood:	n/a	chr16:71757985-71757994 chr16:71757398-71757407
14	POLR2A	chr16:71756992-71758114	HepG2	liver:	n/a	n/a
15	POLR2A	chr16:71756651-71758136	Hela-S3	cervix:	n/a	n/a
16	RCOR1	chr16:71756459-71758468	IMR90	lung:	n/a	n/a
17	POLR2A	chr16:71756757-71758351	Hela-S3	cervix:	n/a	n/a
18	MAZ	chr16:71756566-71758423	IMR90	lung:	n/a	chr16:71757985-71757994 chr16:71757398-71757407
19	POLR2A	chr16:71756859-71758154	A549	lung:	n/a	n/a
20	JUND	chr16:71757389-71757770	K562	blood:	n/a	chr16:71757413-71757422 chr16:71757570-71757579
21	JUND	chr16:71756842-71757435	A549	lung:	n/a	chr16:71757413-71757422
22	GATA1	chr16:71756650-71758722	PBDE	blood:	n/a	chr16:71758249-71758265
23	E2F1	chr16:71756927-71758261	Hela-S3	cervix:	n/a	chr16:71757575-71757585 chr16:71757417-71757426 chr16:71758032-71758041 chr16:71757578-71757588 chr16:71757474-71757483 chr16:71757190-71757199 chr16:71758084-71758096 chr16:71757826-71757835 chr16:71757183-71757193
24	POLR2A	chr16:71756918-71758053	GM12878	blood:	n/a	n/a
25	MAX	chr16:71756582-71758511	A549	lung:	n/a	chr16:71757985-71757994 chr16:71757398-71757407
26	YY1	chr16:71757143-71757852	GM12878	blood:	n/a	chr16:71757537-71757551 chr16:71757581-71757592 chr16:71757574-71757588 chr16:71757574-71757583 chr16:71757199-71757219 chr16:71757572-71757583 chr16:71757568-71757582
27	POLR2A	chr16:71756774-71758145	GM12878	blood:	n/a	n/a
28	POLR2A	chr16:71756840-71758219	GM19193	blood:	n/a	n/a
29	MAX	chr16:71756562-71758473	HepG2	liver:	n/a	chr16:71757985-71757994 chr16:71757398-71757407
30	TFAP2C	chr16:71756605-71758168	Hela-S3	cervix:	n/a	chr16:71757129-71757144
31	HDAC2	chr16:71756695-71757497	MCF-7	breast:	n/a	n/a
32	POLR2A	chr16:71756952-71758132	GM15510	blood:	n/a	n/a
33	POLR2A	chr16:71756923-71757443	PANC-1	pancreas:	n/a	n/a
34	HDAC2	chr16:71756698-71758258	HepG2	liver:	n/a	n/a
35	PAX5	chr16:71756934-71758087	GM12892	blood:	n/a	chr16:71756980-71756999
36	YY1	chr16:71756853-71758141	GM12892	blood:	n/a	chr16:71757537-71757551 chr16:71758032-71758041 chr16:71757581-71757592 chr16:71757574-71757588 chr16:71757574-71757583 chr16:71757199-71757219 chr16:71756981-71756995 chr16:71757931-71757945 chr16:71757937-71757951 chr16:71758120-71758134 chr16:71757572-71757583 chr16:71757568-71757582
37	POLR2A	chr16:71756812-71758221	ECC-1	luminal epithelium:	n/a	n/a
38	MAX	chr16:71756766-71757439	MCF-7	breast:	n/a	chr16:71757398-71757407
39	MAX	chr16:71756628-71758357	Hela-S3	cervix:	n/a	chr16:71757985-71757994 chr16:71757398-71757407
40	POLR2A	chr16:71756677-71758281	Raji	blood:	n/a	n/a
41	POLR2A	chr16:71756810-71758303	GM18505	blood:	n/a	n/a
42	TCF12	chr16:71756522-71757414	A549	lung:	n/a	n/a
43	SIN3AK20	chr16:71756401-71758541	MCF-7	breast:	n/a	n/a
44	POLR2A	chr16:71757327-71757651	GM12891	blood:	n/a	n/a
45	POLR2A	chr16:71756835-71757847	MCF10A-Er-Src	breast:	n/a	n/a
46	ELF1	chr16:71756835-71757820	GM12878	blood:	n/a	chr16:71757540-71757552 chr16:71757580-71757589 chr16:71757575-71757587
47	ZNF263	chr16:71756568-71757741	HEK293-T-REx	kidney:	n/a	chr16:71757023-71757032 chr16:71756792-71756801 chr16:71756888-71756909
48	POLR2A	chr16:71756853-71758114	HUVEC	blood vessel:	n/a	n/a
49	HMGN3	chr16:71756931-71758138	K562	blood:	n/a	n/a
50	POLR2A	chr16:71756759-71757983	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:71756712..71759795-chr16:71768156..71771579,4	MCF-7	breast:
2	chr16:71756383..71758703-chr16:71759355..71761226,2	MCF-7	breast:
3	chr1:6844657..6845258-chr16:71757161..71757923,2	Hela-S3	cervix:
4	chr16:71756102..71758936-chr16:71915033..71919382,3	MCF-7	breast:
5	chr16:71756273..71758753-chr16:71927656..71930818,3	MCF-7	breast:
6	chr16:71755537..71758357-chr16:71878950..71881033,2	K562	blood:
7	chr16:71697444..71699494-chr16:71756866..71759011,2	MCF-7	breast:
8	chr16:71756413..71761113-chr16:71764688..71769079,7	K562	blood:
9	chr16:71748955..71755873-chr16:71756069..71760101,14	MCF-7	breast:
10	chr16:71756422..71758416-chr16:71842004..71843953,2	MCF-7	breast:
11	chr16:71696881..71698945-chr16:71757287..71759170,2	MCF-7	breast:
12	chr16:71756649..71759449-chr16:71879809..71882216,3	MCF-7	breast:
13	chr16:71755635..71758602-chr16:71927230..71929480,2	MCF-7	breast:
14	chr16:71756251..71759040-chr16:71918074..71919809,2	K562	blood:
15	chr16:71658952..71666464-chr16:71755738..71760832,8	MCF-7	breast:
16	chr1:11967125..11969776-chr16:71755847..71757507,2	MCF-7	breast:
17	chr16:71755880..71759578-chr16:71759607..71764621,8	MCF-7	breast:
18	chr16:71756009..71758513-chr16:71878989..71881221,2	K562	blood:
19	chr16:71757196..71759664-chr16:71766555..71771218,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260612	TF binding region
ENSG00000224470	Chromatin interaction
ENSG00000182149	Chromatin interaction
ENSG00000102984	Chromatin interaction
ENSG00000261765	Chromatin interaction
ENSG00000166747	Chromatin interaction
ENSG00000199347	Chromatin interaction
ENSG00000260593	Chromatin interaction
ENSG00000140832	Chromatin interaction
ENSG00000040199	Chromatin interaction
ENSG00000237436	Chromatin interaction
ENSG00000260612	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1058750	0.85[EUR][1000 genomes]
rs10852502	0.85[EUR][1000 genomes]
rs10852503	0.86[EUR][1000 genomes]
rs11075893	0.83[EUR][1000 genomes]
rs11075894	0.88[EUR][1000 genomes]
rs11075898	0.89[EUR][1000 genomes]
rs11075904	0.82[EUR][1000 genomes]
rs11862723	0.89[EUR][1000 genomes]
rs12929547	0.82[EUR][1000 genomes]
rs1392484	0.82[EUR][1000 genomes]
rs1423983	0.88[EUR][1000 genomes]
rs2032918	0.89[EUR][1000 genomes]
rs2052584	0.88[EUR][1000 genomes]
rs2052585	0.86[EUR][1000 genomes]
rs2133773	0.83[EUR][1000 genomes]
rs2334877	0.81[EUR][1000 genomes]
rs2334880	0.86[EUR][1000 genomes]
rs4354946	0.85[EUR][1000 genomes]
rs4788548	0.84[EUR][1000 genomes]
rs4788550	0.88[EUR][1000 genomes]
rs4788553	0.89[EUR][1000 genomes]
rs4788557	0.81[EUR][1000 genomes]
rs4788820	0.83[EUR][1000 genomes]
rs4788822	0.85[EUR][1000 genomes]
rs4788823	0.87[EUR][1000 genomes]
rs4788825	0.86[EUR][1000 genomes]
rs4788828	0.86[EUR][1000 genomes]
rs4788830	0.88[EUR][1000 genomes]
rs6499526	0.85[EUR][1000 genomes]
rs6499527	0.85[EUR][1000 genomes]
rs6499528	0.85[EUR][1000 genomes]
rs6499529	0.89[EUR][1000 genomes]
rs6499530	0.87[EUR][1000 genomes]
rs6499531	0.85[EUR][1000 genomes]
rs6499534	0.91[EUR][1000 genomes]
rs6499538	0.90[EUR][1000 genomes]
rs6499540	0.81[EUR][1000 genomes]
rs7186112	0.80[EUR][1000 genomes]
rs7187948	0.88[EUR][1000 genomes]
rs7188675	0.85[EUR][1000 genomes]
rs7190487	0.84[EUR][1000 genomes]
rs7193549	0.85[EUR][1000 genomes]
rs7195059	0.87[EUR][1000 genomes]
rs7201649	0.82[EUR][1000 genomes]
rs7202479	0.92[EUR][1000 genomes]
rs7204118	0.81[EUR][1000 genomes]
rs7204608	0.85[EUR][1000 genomes]
rs7204967	0.82[EUR][1000 genomes]
rs7204992	0.86[EUR][1000 genomes]
rs7206470	0.86[EUR][1000 genomes]
rs7359478	0.80[EUR][1000 genomes]
rs8044144	0.85[EUR][1000 genomes]
rs8051968	0.87[EUR][1000 genomes]
rs8052910	0.83[EUR][1000 genomes]
rs8053186	0.82[EUR][1000 genomes]
rs8053745	0.87[EUR][1000 genomes]
rs8055419	0.84[EUR][1000 genomes]
rs8058297	0.84[EUR][1000 genomes]
rs8062188	0.88[EUR][1000 genomes]
rs889568	0.84[EUR][1000 genomes]
rs979790	0.85[EUR][1000 genomes]
rs9888756	0.87[EUR][1000 genomes]
rs9929840	0.83[EUR][1000 genomes]
rs9930015	0.84[EUR][1000 genomes]
rs9931074	0.82[EUR][1000 genomes]
rs9934301	0.91[EUR][1000 genomes]
rs9937511	0.81[EUR][1000 genomes]
rs9939458	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3347477	chr16:71555148-71985177	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	esv1817133	chr16:71705908-71837477	ZNF genes & repeats Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer 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	15 gene(s)	inside rSNPs	diseases
3	nsv948468	chr16:71727571-72651914	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS 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	89 gene(s)	inside rSNPs	diseases
4	esv1819402	chr16:71755852-71816899	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers 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	14 gene(s)	inside rSNPs	n/a
5	esv3326836	chr16:71756476-71759024	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	n/a
6	esv3524934	chr16:71756501-71759099	Weak transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	n/a
7	esv3524935	chr16:71756501-71759099	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	n/a
8	esv11117	chr16:71756826-71758273	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12923990	PHLPP2	cis	Muscle Skeletal	GTEx
rs12923990	MARVELD3	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71755600-71758000	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr16:71755800-71758400	Active TSS	NHLF	lung
3	chr16:71756200-71758000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr16:71756200-71758000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr16:71756200-71758000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr16:71756200-71758200	Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr16:71756200-71758200	Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr16:71756200-71758200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
9	chr16:71756200-71758200	Active TSS	Colonic Mucosa	Colon
10	chr16:71756200-71758200	Active TSS	A549	lung
11	chr16:71756200-71758200	Active TSS	HSMM	muscle
12	chr16:71756200-71758400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr16:71756200-71758400	Active TSS	Fetal Kidney	kidney
14	chr16:71756400-71757400	Flanking Active TSS	Primary B cells from cord blood	blood
15	chr16:71756400-71757400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
16	chr16:71756400-71757400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr16:71756400-71758000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr16:71756400-71758000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr16:71756400-71758000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr16:71756400-71758000	Active TSS	Placenta	Placenta
21	chr16:71756400-71758200	Active TSS	ES-I3 Cell Line	embryonic stem cell
22	chr16:71756400-71758200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
23	chr16:71756400-71758200	Active TSS	H1 Cell Line	embryonic stem cell
24	chr16:71756400-71758200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr16:71756400-71758200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr16:71756400-71758200	Active TSS	Brain Germinal Matrix	brain
27	chr16:71756400-71758200	Active TSS	Brain Inferior Temporal Lobe	brain
28	chr16:71756400-71758200	Active TSS	Rectal Mucosa Donor 29	rectum
29	chr16:71756400-71758200	Active TSS	HSMMtube	muscle
30	chr16:71756400-71758200	Active TSS	NHDF-Ad	bronchial
31	chr16:71756400-71758400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr16:71756400-71758400	Active TSS	H9 Cell Line	embryonic stem cell
33	chr16:71756400-71758400	Active TSS	Breast Myoepithelial Primary Cells	Breast
34	chr16:71756600-71757600	Active TSS	Right Atrium	heart
35	chr16:71756600-71758000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr16:71756600-71758000	Active TSS	HUES6 Cell Line	embryonic stem cell
37	chr16:71756600-71758000	Active TSS	Primary T cells fromperipheralblood	blood
38	chr16:71756600-71758000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr16:71756600-71758000	Active TSS	Muscle Satellite Cultured Cells	--
40	chr16:71756600-71758000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr16:71756600-71758000	Active TSS	Fetal Muscle Leg	muscle
42	chr16:71756600-71758000	Active TSS	HMEC	breast
43	chr16:71756600-71758200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr16:71756600-71758200	Active TSS	iPS-18 Cell Line	embryonic stem cell
45	chr16:71756600-71758200	Active TSS	iPS-20b Cell Line	embryonic stem cell
46	chr16:71756600-71758200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr16:71756600-71758200	Active TSS	Aorta	Aorta
48	chr16:71756600-71758200	Active TSS	Colon Smooth Muscle	Colon
49	chr16:71756600-71758200	Active TSS	Ovary	ovary
50	chr16:71756600-71758200	Active TSS	Right Ventricle	heart

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