Variant report

Variant	rs11860057
Chromosome Location	chr16:79804773-79804774
allele	A/C
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	RFX5	chr16:79803570-79805472	IMR90	lung:	n/a	chr16:79804613-79804622 chr16:79804610-79804625 chr16:79804611-79804625
2	HA-E2F1	chr16:79804185-79804950	MCF-7	breast:	n/a	chr16:79804587-79804602 chr16:79804591-79804605 chr16:79804656-79804666 chr16:79804457-79804466 chr16:79804816-79804833
3	NFYB	chr16:79804190-79804982	K562	blood:	n/a	chr16:79804631-79804645 chr16:79804628-79804643 chr16:79804631-79804646 chr16:79804631-79804646 chr16:79804597-79804612
4	MXI1	chr16:79803755-79805133	SK-N-SH	brain:	n/a	n/a
5	IRF1	chr16:79804005-79804899	K562	blood:	n/a	chr16:79804465-79804479
6	ZMIZ1	chr16:79803430-79805584	K562	blood:	n/a	n/a
7	BACH1	chr16:79804668-79804851	K562	blood:	n/a	n/a
8	JUND	chr16:79804003-79805046	K562	blood:	n/a	chr16:79804470-79804479 chr16:79804635-79804644
9	NFYB	chr16:79804412-79804937	GM12878	blood:	n/a	chr16:79804631-79804645 chr16:79804628-79804643 chr16:79804631-79804646 chr16:79804631-79804646 chr16:79804597-79804612
10	SP1	chr16:79804304-79804986	H1-hESC	embryonic stem cell:	n/a	chr16:79804467-79804479 chr16:79804632-79804653 chr16:79804468-79804477 chr16:79804468-79804477 chr16:79804469-79804478 chr16:79804467-79804479
11	MAX	chr16:79803909-79804981	K562	blood:	n/a	n/a
12	POLR2A	chr16:79803019-79805255	K562	blood:	n/a	n/a
13	EP300	chr16:79804342-79804835	SK-N-SH_RA	brain:	n/a	n/a
14	EP300	chr16:79802602-79805391	SK-N-SH	brain:	n/a	chr16:79802820-79802834 chr16:79803941-79803955 chr16:79802825-79802839
15	E2F4	chr16:79804360-79804938	MCF10A-Er-Src	breast:	n/a	chr16:79804587-79804602 chr16:79804591-79804605 chr16:79804656-79804666 chr16:79804457-79804466 chr16:79804816-79804833
16	NFYA	chr16:79804237-79805394	K562	blood:	n/a	chr16:79804631-79804645 chr16:79804631-79804646 chr16:79804631-79804646
17	CUX1	chr16:79804659-79805310	K562	blood:	n/a	n/a
18	FOS	chr16:79804421-79804845	K562	blood:	n/a	chr16:79804470-79804479 chr16:79804635-79804644
19	ZNF143	chr16:79803992-79804914	K562	blood:	n/a	n/a
20	SRF	chr16:79804647-79804935	K562	blood:	n/a	chr16:79804656-79804666
21	UBTF	chr16:79804168-79804937	K562	blood:	n/a	n/a
22	ATF3	chr16:79804703-79804877	K562	blood:	n/a	n/a
23	RAD21	chr16:79804186-79804794	H1-hESC	embryonic stem cell:	n/a	n/a
24	YY1	chr16:79804449-79804916	K562	blood:	n/a	chr16:79804461-79804472 chr16:79804455-79804469
25	POLR2A	chr16:79803975-79804829	GM19193	blood:	n/a	n/a
26	HMGN3	chr16:79804031-79804893	K562	blood:	n/a	n/a
27	POLR2A	chr16:79803948-79805011	K562	blood:	n/a	n/a
28	RCOR1	chr16:79803960-79804909	K562	blood:	n/a	n/a
29	MAZ	chr16:79803269-79804943	K562	blood:	n/a	n/a
30	RAD21	chr16:79804167-79804790	H1-hESC	embryonic stem cell:	n/a	n/a
31	MAX	chr16:79804675-79804913	K562	blood:	n/a	n/a
32	CREB1	chr16:79804075-79804850	A549	lung:	n/a	n/a
33	BHLHE40	chr16:79804474-79804778	GM12878	blood:	n/a	n/a
34	POLR2A	chr16:79803767-79805282	K562	blood:	n/a	n/a
35	EP300	chr16:79804034-79805202	K562	blood:	n/a	n/a
36	ELK1	chr16:79804713-79804841	K562	blood:	n/a	n/a
37	HCFC1	chr16:79804071-79805048	K562	blood:	n/a	n/a
38	POLR2A	chr16:79804595-79804876	K562	blood:	n/a	n/a
39	TCF7L2	chr16:79804276-79804796	MCF-7	breast:	n/a	n/a
40	TBL1XR1	chr16:79804010-79804970	K562	blood:	n/a	n/a
41	REST	chr16:79804637-79804919	K562	blood:	n/a	n/a
42	SP1	chr16:79804412-79804869	H1-hESC	embryonic stem cell:	n/a	chr16:79804467-79804479 chr16:79804632-79804653 chr16:79804468-79804477 chr16:79804468-79804477 chr16:79804469-79804478 chr16:79804467-79804479
43	POLR2A	chr16:79803997-79804958	K562	blood:	n/a	n/a
44	MAX	chr16:79803928-79805047	MCF-7	breast:	n/a	n/a
45	IRF1	chr16:79804240-79805006	K562	blood:	n/a	chr16:79804465-79804479
46	SP1	chr16:79804297-79804871	A549	lung:	n/a	chr16:79804467-79804479 chr16:79804632-79804653 chr16:79804468-79804477 chr16:79804468-79804477 chr16:79804469-79804478 chr16:79804467-79804479
47	RFX5	chr16:79804085-79805420	HepG2	liver:	n/a	chr16:79804613-79804622 chr16:79804610-79804625 chr16:79804611-79804625
48	BHLHE40	chr16:79803209-79805113	K562	blood:	n/a	n/a
49	ZNF384	chr16:79804159-79804779	GM12878	blood:	n/a	n/a
50	HEY1	chr16:79804549-79804892	K562	blood:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MAF-2	chr16:79804344-79804827	XLOC_012017

Variant related genes	Relation type
ENSG00000261390	TF binding region

Extended variants
information (count: 76 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10871378	0.81[EUR][1000 genomes]
rs11150215	0.82[AFR][1000 genomes]
rs12448881	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13337701	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13337703	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13338008	0.91[EUR][1000 genomes]
rs13338235	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16951312	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16951359	0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28536718	0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4243180	0.88[ASN][1000 genomes]
rs4296269	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4302049	0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4316769	0.89[ASN][1000 genomes]
rs4319779	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4319782	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4372706	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4470160	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4474702	0.86[ASN][1000 genomes]
rs4528586	0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4547344	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4567730	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4567731	0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4603571	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4614737	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4632146	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4633733	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4889024	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4889026	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59100419	0.87[ASN][1000 genomes]
rs59680118	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60153062	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62041321	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62041342	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62041343	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6564697	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6564698	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6564702	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6564703	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6564704	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs66616635	0.88[ASN][1000 genomes]
rs67364537	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7187216	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7188433	0.88[ASN][1000 genomes]
rs7190102	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7199398	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7200937	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7202532	0.88[ASN][1000 genomes]
rs7205712	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73572226	0.86[ASN][1000 genomes]
rs8052982	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8053230	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8056805	0.81[ASN][1000 genomes]
rs8057083	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8057344	0.81[ASN][1000 genomes]
rs8060072	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8062324	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8063650	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9673780	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9922033	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9925997	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9927594	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9927598	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9928163	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9929497	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9931431	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9936175	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9936192	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9936261	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9939090	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9939565	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv573285	chr16:79158182-80127326	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv530714	chr16:79661581-79925435	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv833296	chr16:79692236-79889727	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv833297	chr16:79732501-79920419	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	esv2755409	chr16:79776699-79816299	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11860057	RP11-345M22.1	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:79801400-79805000	Enhancers	Placenta Amnion	Placenta Amnion
2	chr16:79803600-79805200	Flanking Active TSS	Adipose Nuclei	Adipose
3	chr16:79803600-79805200	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr16:79803800-79804800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr16:79803800-79804800	Active TSS	Fetal Brain Female	brain
6	chr16:79803800-79804800	Active TSS	Rectal Mucosa Donor 29	rectum
7	chr16:79803800-79805000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr16:79803800-79805000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr16:79803800-79805200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr16:79804000-79804800	Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr16:79804000-79804800	Active TSS	iPS-18 Cell Line	embryonic stem cell
12	chr16:79804000-79804800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr16:79804000-79804800	Active TSS	Primary T helper naive cells from peripheral blood	blood
14	chr16:79804000-79804800	Active TSS	Brain Anterior Caudate	brain
15	chr16:79804000-79804800	Active TSS	Fetal Kidney	kidney
16	chr16:79804000-79804800	Active TSS	Thymus	Thymus
17	chr16:79804000-79804800	Active TSS	GM12878-XiMat	blood
18	chr16:79804000-79804800	Active TSS	HSMM	muscle
19	chr16:79804000-79804800	Active TSS	Monocytes-CD14+_RO01746	blood
20	chr16:79804000-79805000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr16:79804000-79805000	Active TSS	H9 Cell Line	embryonic stem cell
22	chr16:79804000-79805000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr16:79804000-79805000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr16:79804000-79805000	Active TSS	HUES6 Cell Line	embryonic stem cell
25	chr16:79804000-79805000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr16:79804000-79805000	Active TSS	iPS-20b Cell Line	embryonic stem cell
27	chr16:79804000-79805000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr16:79804000-79805000	Flanking Active TSS	Primary B cells from peripheral blood	blood
29	chr16:79804000-79805000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
30	chr16:79804000-79805000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr16:79804000-79805000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
32	chr16:79804000-79805000	Active TSS	Brain Germinal Matrix	brain
33	chr16:79804000-79805000	Active TSS	Psoas Muscle	Psoas
34	chr16:79804000-79805000	Active TSS	HSMMtube	muscle
35	chr16:79804000-79805200	Active TSS	ES-I3 Cell Line	embryonic stem cell
36	chr16:79804000-79805200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr16:79804000-79805200	Active TSS	HUES64 Cell Line	embryonic stem cell
38	chr16:79804000-79805200	Flanking Active TSS	Primary hematopoietic stem cells	blood
39	chr16:79804000-79805200	Active TSS	Aorta	Aorta
40	chr16:79804000-79805200	Active TSS	Ovary	ovary
41	chr16:79804200-79804800	Active TSS	H1 Cell Line	embryonic stem cell
42	chr16:79804200-79804800	Active TSS	Breast Myoepithelial Primary Cells	Breast
43	chr16:79804200-79804800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
44	chr16:79804200-79804800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
45	chr16:79804200-79804800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
46	chr16:79804200-79804800	Active TSS	Primary T helper cells PMA-I stimulated	--
47	chr16:79804200-79804800	Active TSS	Muscle Satellite Cultured Cells	--
48	chr16:79804200-79804800	Active TSS	Cortex derived primary cultured neurospheres	brain
49	chr16:79804200-79804800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr16:79804200-79804800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin

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