Variant report

Variant	rs3813002
Chromosome Location	chr16:31470540-31470541
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	E2F4	chr16:31470430-31471597	MCF10A-Er-Src	breast:	n/a	chr16:31470735-31470750 chr16:31471234-31471242 chr16:31471472-31471481 chr16:31471470-31471479 chr16:31470482-31470491
2	CEBPB	chr16:31470528-31471635	HepG2	liver:	n/a	n/a
3	MYC	chr16:31469259-31471590	K562	blood:	n/a	chr16:31471466-31471475 chr16:31469553-31469569
4	CEBPB	chr16:31470462-31471001	MCF-7	breast:	n/a	n/a
5	YY1	chr16:31470207-31471233	GM12892	blood:	n/a	chr16:31470841-31470853 chr16:31470835-31470855 chr16:31470482-31470491
6	POLR2A	chr16:31469912-31471556	A549	lung:	n/a	n/a
7	TAF1	chr16:31470220-31471109	GM12878	blood:	n/a	n/a
8	CTCF	chr16:31468918-31472489	A549	lung:	n/a	chr16:31470418-31470436 chr16:31472184-31472202 chr16:31472186-31472199 chr16:31472179-31472200 chr16:31469573-31469586 chr16:31472185-31472201
9	ELF1	chr16:31470070-31471581	SK-N-SH	brain:	n/a	chr16:31470690-31470701 chr16:31470690-31470701 chr16:31470691-31470700
10	RAD21	chr16:31470301-31470707	HepG2	liver:	n/a	n/a
11	CEBPB	chr16:31470324-31471619	HepG2	liver:	n/a	n/a
12	RFX5	chr16:31470248-31471668	Hela-S3	cervix:	n/a	n/a
13	ELF1	chr16:31469172-31471469	GM12878	blood:	n/a	chr16:31470690-31470701 chr16:31470690-31470701 chr16:31470691-31470700
14	CTCF	chr16:31469194-31470976	K562	blood:	n/a	chr16:31470418-31470436 chr16:31469573-31469586
15	GABPA	chr16:31470028-31471576	SK-N-SH	brain:	n/a	chr16:31470482-31470491
16	FOXP2	chr16:31470469-31471440	SK-N-MC	brain:	n/a	n/a
17	CTCF	chr16:31470289-31470562	MCF-7	breast:	n/a	chr16:31470418-31470436
18	CTCF	chr16:31470161-31470777	IMR90	lung:	n/a	chr16:31470418-31470436
19	TCF12	chr16:31470475-31470913	GM12878	blood:	n/a	n/a
20	SIN3AK20	chr16:31470224-31471141	K562	blood:	n/a	n/a
21	ZC3H11A	chr16:31470234-31470993	K562	blood:	n/a	n/a
22	TCF7L2	chr16:31470245-31471501	HCT-116	colon:	n/a	n/a
23	MAX	chr16:31470226-31471219	H1-hESC	embryonic stem cell:	n/a	n/a
24	SMC3	chr16:31469236-31471626	Hela-S3	cervix:	n/a	n/a
25	UBTF	chr16:31469047-31471023	K562	blood:	n/a	n/a
26	PAX5	chr16:31470182-31470976	GM12878	blood:	n/a	chr16:31470427-31470445
27	POLR2A	chr16:31469212-31471516	GM12878	blood:	n/a	n/a
28	GATA1	chr16:31470340-31472018	PBDE	blood:	n/a	n/a
29	RCOR1	chr16:31470074-31471484	HepG2	liver:	n/a	n/a
30	HEY1	chr16:31469204-31471566	K562	blood:	n/a	chr16:31470134-31470149 chr16:31470084-31470099 chr16:31471470-31471479 chr16:31471472-31471481
31	POLR2A	chr16:31469329-31472087	K562	blood:	n/a	n/a
32	MXI1	chr16:31469217-31471568	HepG2	liver:	n/a	chr16:31469405-31469414
33	HCFC1	chr16:31469109-31471948	Hela-S3	cervix:	n/a	n/a
34	MYC	chr16:31469225-31471598	K562	blood:	n/a	chr16:31471466-31471475 chr16:31469553-31469569
35	CREB1	chr16:31470325-31471752	H1-hESC	embryonic stem cell:	n/a	chr16:31471469-31471482
36	CTCF	chr16:31470305-31470543	NHEK	skin:	n/a	chr16:31470418-31470436
37	PML	chr16:31470208-31471621	MCF-7	breast:	n/a	n/a
38	ZEB1	chr16:31470244-31470805	GM12878	blood:	n/a	n/a
39	POU2F2	chr16:31470332-31471108	GM12891	blood:	n/a	n/a
40	POLR2A	chr16:31469283-31471622	K562	blood:	n/a	n/a
41	REST	chr16:31469793-31472299	H1-neurons	neurons:	n/a	chr16:31470354-31470368 chr16:31470745-31470752
42	YY1	chr16:31470478-31471194	GM12891	blood:	n/a	chr16:31470841-31470853 chr16:31470835-31470855 chr16:31470482-31470491
43	SIN3AK20	chr16:31469065-31471835	MCF-7	breast:	n/a	n/a
44	RELA	chr16:31469245-31471056	GM19099	blood:	n/a	n/a
45	POLR2A	chr16:31470072-31471485	A549	lung:	n/a	n/a
46	MAX	chr16:31469949-31471214	A549	lung:	n/a	n/a
47	CTCF	chr16:31470420-31470570	HMEC	breast:	n/a	n/a
48	TAF1	chr16:31470034-31471590	ECC-1	luminal epithelium:	n/a	n/a
49	CEBPB	chr16:31470540-31470880	A549	lung:	n/a	n/a
50	MAX	chr16:31469338-31471514	GM12878	blood:	n/a	chr16:31471466-31471475 chr16:31469553-31469569

No.	Distal block	Cell Line	Cell type
1	chr16:31190494..31194030-chr16:31469173..31472392,6	MCF-7	breast:
2	chr12:54673440..54674342-chr16:31470299..31471188,2	Hela-S3	cervix:
3	chr16:31468972..31472729-chr16:31517678..31523478,11	K562	blood:
4	chr16:31453063..31456087-chr16:31468584..31471837,4	K562	blood:
5	chr16:31470533..31471081-chr7:54826331..54826933,2	Hela-S3	cervix:
6	chr16:31469520..31471789-chr16:31495046..31498029,3	MCF-7	breast:
7	chr16:30967074..30970924-chr16:31469051..31472537,7	K562	blood:
8	chr16:30995577..30998794-chr16:31467620..31471183,4	MCF-7	breast:
9	chr16:30967183..30971961-chr16:31469060..31471569,4	MCF-7	breast:
10	chr16:31468140..31471133-chr16:31724477..31727489,3	K562	blood:
11	chr16:31465649..31475592-chr16:31481764..31491028,24	MCF-7	breast:
12	chr16:8890468..8892714-chr16:31469451..31471408,2	MCF-7	breast:
13	chr16:31463366..31472153-chr16:31517209..31524290,14	MCF-7	breast:
14	chr16:31190035..31193017-chr16:31469730..31472646,5	K562	blood:
15	chr1:155904020..155904915-chr16:31470297..31470850,2	Hela-S3	cervix:
16	chr16:31189995..31193017-chr16:31468555..31472249,11	K562	blood:
17	chr16:31210690..31213656-chr16:31469495..31472213,2	MCF-7	breast:
18	chr16:31467317..31473648-chr16:31720179..31727010,13	MCF-7	breast:
19	chr16:31468059..31475073-chr16:31494279..31502185,17	MCF-7	breast:
20	chr16:31467955..31471666-chr16:31883019..31886709,4	MCF-7	breast:
21	chr10:5708283..5708927-chr16:31470241..31471151,2	Hela-S3	cervix:
22	chr16:31466906..31472700-chr16:31708858..31713293,7	K562	blood:
23	chr16:31117883..31120430-chr16:31468936..31471435,2	MCF-7	breast:
24	chr16:31453017..31458651-chr16:31467711..31471563,6	K562	blood:
25	chr16:31469614..31471877-chr16:31713296..31715229,2	K562	blood:
26	chr16:31082772..31088721-chr16:31466605..31471958,8	MCF-7	breast:
27	chr16:31468357..31473774-chr16:31516772..31522690,14	K562	blood:
28	chr16:31470147..31470880-chr2:232378653..232379343,2	Hela-S3	cervix:
29	chr16:31470457..31470968-chr17:47865791..47866377,2	HCT-116	colon:
30	chr16:31469955..31470731-chr7:23509762..23510727,2	Hela-S3	cervix:
31	chr16:31470284..31471058-chr17:75283807..75284397,2	Hela-S3	cervix:
32	chr16:31470167..31471161-chrX:11129379..11129924,2	Hela-S3	cervix:
33	chr16:31466606..31474995-chr16:31481116..31490982,25	MCF-7	breast:
34	chr16:31470148..31471078-chr17:48943816..48944445,2	Hela-S3	cervix:
35	chr16:31470460..31470990-chr20:43104311..43104986,2	Hela-S3	cervix:
36	chr16:31127569..31130475-chr16:31469319..31471867,2	K562	blood:
37	chr16:31144729..31147101-chr16:31468783..31472042,3	MCF-7	breast:
38	chr16:30968652..30970204-chr16:31469437..31471305,2	MCF-7	breast:
39	chr16:30886288..30887012-chr16:31470235..31471093,2	HCT-116	colon:
40	chr16:31468593..31471652-chr16:31724469..31726799,3	K562	blood:
41	chr11:62608717..62609620-chr16:31470316..31471600,4	Hela-S3	cervix:
42	chr13:96329295..96329836-chr16:31470265..31470990,2	Hela-S3	cervix:
43	chr16:30967074..30970924-chr16:31469051..31472279,6	K562	blood:
44	chr16:31469667..31470562-chr17:7387286..7388085,2	Hela-S3	cervix:
45	chr16:31468309..31472565-chr16:31709404..31716221,13	MCF-7	breast:
46	chr16:31083053..31086141-chr16:31468278..31470995,4	MCF-7	breast:
47	chr1:149857567..149858265-chr16:31470499..31471217,2	Hela-S3	cervix:
48	chr16:31469119..31472117-chr6:86351411..86353551,2	MCF-7	breast:
49	chr16:31470071..31470956-chr6:36561864..36562752,2	Hela-S3	cervix:
50	chr16:31468899..31473390-chr16:31518411..31522821,12	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF843-2	chr16:31468032-31471057	ENSG00000260267.1

Variant related genes	Relation type
ARMC5	TF binding region
ENSG00000136231	Chromatin interaction
ENSG00000103510	Chromatin interaction
ENSG00000184678	Chromatin interaction
ENSG00000181222	Chromatin interaction
ENSG00000140682	Chromatin interaction
ENSG00000270022	Chromatin interaction
ENSG00000131797	Chromatin interaction
ENSG00000262766	Chromatin interaction
ENSG00000260625	Chromatin interaction
ENSG00000100227	Chromatin interaction
ENSG00000099377	Chromatin interaction
ENSG00000260083	Chromatin interaction
ENSG00000102580	Chromatin interaction
ENSG00000132680	Chromatin interaction
ENSG00000185947	Chromatin interaction
ENSG00000094916	Chromatin interaction
ENSG00000121104	Chromatin interaction
ENSG00000229980	Chromatin interaction
ENSG00000135486	Chromatin interaction
ENSG00000261731	Chromatin interaction
ENSG00000140675	Chromatin interaction
ENSG00000140650	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000089280	Chromatin interaction
ENSG00000112081	Chromatin interaction
ENSG00000099381	Chromatin interaction
ENSG00000260472	Chromatin interaction
ENSG00000052344	Chromatin interaction
ENSG00000181798	Chromatin interaction
ENSG00000184857	Chromatin interaction
ENSG00000136504	Chromatin interaction
ENSG00000176723	Chromatin interaction
ENSG00000268863	Chromatin interaction
ENSG00000265991	Chromatin interaction
ENSG00000184640	Chromatin interaction
ENSG00000261359	Chromatin interaction
ENSG00000197302	Chromatin interaction
ENSG00000196372	Chromatin interaction
ENSG00000116560	Chromatin interaction
ENSG00000140688	Chromatin interaction
ENSG00000167395	Chromatin interaction
ENSG00000135316	Chromatin interaction
ENSG00000132432	Chromatin interaction
ENSG00000124120	Chromatin interaction
ENSG00000260568	Chromatin interaction
ENSG00000167394	Chromatin interaction
ENSG00000103507	Chromatin interaction
ENSG00000174282	Chromatin interaction
ENSG00000004961	Chromatin interaction
ENSG00000260740	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs11150625	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4536493	0.85[CEU][hapmap];0.89[CHB][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.80[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4889659	0.92[CEU][hapmap]
rs9927250	0.95[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3392534	chr16:31303038-31573066	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	104 gene(s)	inside rSNPs	diseases
2	nsv833194	chr16:31358179-31528545	Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	97 gene(s)	inside rSNPs	diseases
3	nsv905747	chr16:31394179-31888684	Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	123 gene(s)	inside rSNPs	diseases
4	nsv905748	chr16:31427678-31559220	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	94 gene(s)	inside rSNPs	diseases
5	nsv905749	chr16:31427678-31565597	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	96 gene(s)	inside rSNPs	diseases
6	nsv905750	chr16:31427678-31587662	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	98 gene(s)	inside rSNPs	diseases
7	nsv905751	chr16:31431360-31489033	Bivalent Enhancer Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	82 gene(s)	inside rSNPs	diseases
8	nsv905752	chr16:31436932-31565597	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	95 gene(s)	inside rSNPs	diseases
9	nsv905753	chr16:31436932-31587662	Enhancers Active TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	97 gene(s)	inside rSNPs	diseases
10	nsv905754	chr16:31451699-31565597	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	93 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3813002	TGFB1I1	cis	cerebellum	SCAN
rs3813002	RABEP2	cis	parietal	SCAN
rs3813002	CD19	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:31468600-31470600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr16:31468600-31470600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr16:31468600-31472000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr16:31468800-31471600	Active TSS	A549	lung
5	chr16:31469000-31470600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
6	chr16:31469000-31471000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
7	chr16:31469000-31471400	Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr16:31469000-31471600	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr16:31469000-31471600	Active TSS	Psoas Muscle	Psoas
10	chr16:31469000-31471600	Active TSS	HSMMtube	muscle
11	chr16:31469000-31472000	Active TSS	H9 Cell Line	embryonic stem cell
12	chr16:31469000-31472000	Active TSS	HUES48 Cell Line	embryonic stem cell
13	chr16:31469000-31472000	Active TSS	HUES64 Cell Line	embryonic stem cell
14	chr16:31469000-31472000	Active TSS	iPS-18 Cell Line	embryonic stem cell
15	chr16:31469000-31472000	Active TSS	iPS-20b Cell Line	embryonic stem cell
16	chr16:31469200-31470600	Flanking Active TSS	Primary B cells from cord blood	blood
17	chr16:31469200-31470600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
18	chr16:31469200-31470600	Flanking Active TSS	Primary hematopoietic stem cells	blood
19	chr16:31469200-31470600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
20	chr16:31469200-31470600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
21	chr16:31469200-31471800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr16:31469200-31471800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr16:31469200-31472000	Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr16:31469400-31470600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
25	chr16:31469400-31470600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr16:31469400-31471000	Active TSS	Small Intestine	intestine
27	chr16:31469400-31471400	Active TSS	Fetal Intestine Small	intestine
28	chr16:31469400-31471400	Active TSS	NHDF-Ad	bronchial
29	chr16:31469400-31471600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr16:31469400-31471600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr16:31469400-31471600	Active TSS	Fetal Intestine Large	intestine
32	chr16:31469400-31471800	Active TSS	Ovary	ovary
33	chr16:31469400-31472000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr16:31469400-31472200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr16:31469600-31471200	Active TSS	Sigmoid Colon	Sigmoid Colon
36	chr16:31469600-31471400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr16:31469600-31471400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr16:31469600-31471400	Active TSS	Primary T helper cells PMA-I stimulated	--
39	chr16:31469600-31471400	Active TSS	Muscle Satellite Cultured Cells	--
40	chr16:31469600-31471400	Active TSS	Liver	Liver
41	chr16:31469600-31471400	Active TSS	Duodenum Mucosa	Duodenum
42	chr16:31469600-31471400	Active TSS	Pancreas	Pancrea
43	chr16:31469600-31471400	Active TSS	Stomach Mucosa	stomach
44	chr16:31469600-31471400	Active TSS	Hela-S3	cervix
45	chr16:31469600-31471600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr16:31469600-31471600	Active TSS	Breast Myoepithelial Primary Cells	Breast
47	chr16:31469600-31471600	Active TSS	Colon Smooth Muscle	Colon
48	chr16:31469600-31471600	Active TSS	Fetal Heart	heart
49	chr16:31469600-31471600	Active TSS	Gastric	stomach
50	chr16:31469600-31471600	Active TSS	Left Ventricle	heart

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