Variant report

Variant	rs11685107
Chromosome Location	chr2:114040583-114040584
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	EP300	chr2:114040355-114042007	A549	lung:	n/a	chr2:114041601-114041617
2	REST	chr2:114040420-114040965	HepG2	liver:	n/a	chr2:114040737-114040750
3	POLR2A	chr2:114040475-114040852	A549	lung:	n/a	n/a
4	NFIC	chr2:114039914-114041352	HepG2	liver:	n/a	n/a
5	TCF12	chr2:114040512-114040987	A549	lung:	n/a	n/a
6	BHLHE40	chr2:114040418-114041081	HepG2	liver:	n/a	n/a
7	RAD21	chr2:114040553-114040990	HepG2	liver:	n/a	chr2:114040837-114040851 chr2:114040700-114040712 chr2:114040838-114040857 chr2:114040700-114040710
8	POLR2A	chr2:114040416-114040864	HepG2	liver:	n/a	n/a
9	EP300	chr2:114040470-114042086	ECC-1	luminal epithelium:	n/a	chr2:114042041-114042048 chr2:114041601-114041617
10	POLR2A	chr2:114040002-114042969	U87	brain:	n/a	n/a
11	GATA3	chr2:114040064-114041988	A549	lung:	n/a	chr2:114040943-114040953
12	MXI1	chr2:114040085-114041099	HepG2	liver:	n/a	chr2:114040778-114040787
13	MBD4	chr2:114039913-114041064	HepG2	liver:	n/a	n/a
14	HDAC2	chr2:114040028-114041071	HepG2	liver:	n/a	n/a
15	HDAC2	chr2:114040250-114041040	HepG2	liver:	n/a	n/a
16	SRF	chr2:114040457-114041013	ECC-1	luminal epithelium:	n/a	n/a
17	POLR2A	chr2:114040467-114040858	HepG2	liver:	n/a	n/a
18	MAX	chr2:114039937-114040993	HepG2	liver:	n/a	chr2:114040779-114040788 chr2:114040778-114040788 chr2:114040779-114040788 chr2:114040777-114040785 chr2:114040778-114040789 chr2:114040206-114040215 chr2:114040779-114040788
19	MAX	chr2:114040326-114041270	ECC-1	luminal epithelium:	n/a	chr2:114040779-114040788 chr2:114040778-114040788 chr2:114040779-114040788 chr2:114040777-114040785 chr2:114040778-114040789 chr2:114040779-114040788
20	MAX	chr2:114040565-114041017	H1-hESC	embryonic stem cell:	n/a	chr2:114040779-114040788 chr2:114040778-114040788 chr2:114040779-114040788 chr2:114040777-114040785 chr2:114040778-114040789 chr2:114040779-114040788
21	CEBPB	chr2:114040146-114040965	HepG2	liver:	n/a	n/a
22	E2F6	chr2:114040365-114041180	A549	lung:	n/a	n/a
23	FOXM1	chr2:114040291-114042129	ECC-1	luminal epithelium:	n/a	n/a
24	USF2	chr2:114040549-114040965	HepG2	liver:	n/a	n/a
25	ARID3A	chr2:114040264-114041172	HepG2	liver:	n/a	n/a
26	HEY1	chr2:114039910-114041181	HepG2	liver:	n/a	n/a
27	TBP	chr2:114040218-114041039	HepG2	liver:	n/a	n/a
28	MYC	chr2:114040416-114041801	MCF10A-Er-Src	breast:	n/a	chr2:114040779-114040788 chr2:114040778-114040788 chr2:114040779-114040788 chr2:114040777-114040785 chr2:114040778-114040789 chr2:114040779-114040788
29	MAX	chr2:114039577-114042272	A549	lung:	n/a	chr2:114040779-114040788 chr2:114040778-114040788 chr2:114040779-114040788 chr2:114040777-114040785 chr2:114040778-114040789 chr2:114040206-114040215 chr2:114040779-114040788
30	SP1	chr2:114039766-114041029	HepG2	liver:	n/a	chr2:114040737-114040751 chr2:114039879-114039889
31	ATF3	chr2:114040459-114040953	A549	lung:	n/a	n/a
32	POLR2A	chr2:114040341-114040861	U87	brain:	n/a	n/a
33	EP300	chr2:114040233-114041074	HepG2	liver:	n/a	n/a
34	TEAD4	chr2:114040399-114041183	ECC-1	luminal epithelium:	n/a	n/a
35	POLR2A	chr2:114040499-114041102	ECC-1	luminal epithelium:	n/a	n/a
36	MYC	chr2:114040510-114041028	NB4	blood:	n/a	chr2:114040779-114040788 chr2:114040778-114040788 chr2:114040779-114040788 chr2:114040777-114040785 chr2:114040778-114040789 chr2:114040779-114040788
37	HNF4A	chr2:114040333-114040892	HepG2	liver:	n/a	chr2:114040449-114040461 chr2:114040448-114040462 chr2:114040448-114040463 chr2:114040448-114040461
38	CEBPB	chr2:114040315-114041768	A549	lung:	n/a	n/a
39	TAF1	chr2:114040492-114041057	ECC-1	luminal epithelium:	n/a	n/a
40	ELF1	chr2:114040564-114041017	A549	lung:	n/a	n/a
41	E2F6	chr2:114040565-114041020	A549	lung:	n/a	n/a
42	JUND	chr2:114040229-114040998	A549	lung:	n/a	n/a
43	RAD21	chr2:114040448-114041017	HepG2	liver:	n/a	chr2:114040837-114040851 chr2:114040700-114040712 chr2:114040838-114040857 chr2:114040700-114040710
44	USF1	chr2:114040488-114041024	ECC-1	luminal epithelium:	n/a	n/a
45	POLR2A	chr2:114040420-114040925	A549	lung:	n/a	n/a
46	CEBPB	chr2:114040436-114041082	ECC-1	luminal epithelium:	n/a	n/a
47	USF1	chr2:114040582-114041074	ECC-1	luminal epithelium:	n/a	n/a
48	MAX	chr2:114040564-114041039	MCF-7	breast:	n/a	chr2:114040779-114040788 chr2:114040778-114040788 chr2:114040779-114040788 chr2:114040777-114040785 chr2:114040778-114040789 chr2:114040779-114040788
49	NR3C1	chr2:114040397-114040960	A549	lung:	n/a	chr2:114040741-114040754
50	SP1	chr2:114040282-114042083	A549	lung:	n/a	chr2:114040737-114040751

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:114033208..114035776-chr2:114039656..114042402,2	K562	blood:

Variant related genes	Relation type
PAX8	TF binding region

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10864913	0.88[AMR][1000 genomes]
rs11123176	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11123177	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11123179	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11685421	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11691437	0.81[ASN][1000 genomes]
rs11695071	0.88[AMR][1000 genomes]
rs12475140	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12476056	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12476331	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12478795	0.81[ASN][1000 genomes]
rs12999288	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs13015130	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1900216	0.81[ASN][1000 genomes]
rs2002510	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35006857	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs36000169	0.86[AMR][1000 genomes]
rs4848321	0.81[ASN][1000 genomes]
rs6716573	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7425070	0.88[AMR][1000 genomes]
rs877202	0.81[ASN][1000 genomes]
rs895416	0.81[ASN][1000 genomes]
rs895417	0.81[ASN][1000 genomes]
rs935365	0.81[ASN][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	nsv508162	chr2:113983043-114099966	Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv874901	chr2:114022569-114079565	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv998204	chr2:114023917-114075446	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11685107	LOC654433	Cis_1M	lymphoblastoid	RTeQTL
rs11685107	AC016683.6	cis	lung	GTEx

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:114036600-114043800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:114037400-114040600	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr2:114037400-114043600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr2:114037600-114042200	Enhancers	Pancreas	Pancrea
5	chr2:114037600-114043800	Enhancers	HMEC	breast
6	chr2:114038200-114043800	Enhancers	Fetal Intestine Large	intestine
7	chr2:114038400-114043600	Enhancers	Fetal Intestine Small	intestine
8	chr2:114038600-114040800	Enhancers	NHEK	skin
9	chr2:114038600-114043600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr2:114038600-114043800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr2:114039000-114040600	Weak transcription	NHDF-Ad	bronchial
12	chr2:114039000-114041400	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr2:114039000-114043800	Enhancers	HSMM	muscle
14	chr2:114039200-114041800	Enhancers	Muscle Satellite Cultured Cells	--
15	chr2:114039400-114041800	Enhancers	NH-A	brain
16	chr2:114039400-114042000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr2:114039400-114043000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr2:114039400-114043200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr2:114039400-114043200	Enhancers	Placenta Amnion	Placenta Amnion
20	chr2:114039600-114041400	Flanking Active TSS	A549	lung
21	chr2:114039600-114042200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr2:114039600-114042400	Enhancers	Adipose Nuclei	Adipose
23	chr2:114039600-114042600	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr2:114039600-114043400	Enhancers	Osteobl	bone
25	chr2:114039600-114043600	Enhancers	HSMMtube	muscle
26	chr2:114039600-114043800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr2:114039800-114040600	Enhancers	Gastric	stomach
28	chr2:114039800-114041200	Enhancers	Lung	lung
29	chr2:114039800-114041400	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
30	chr2:114039800-114042200	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr2:114039800-114042200	Enhancers	Stomach Mucosa	stomach
32	chr2:114039800-114043600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr2:114040000-114040600	Flanking Active TSS	Liver	Liver
34	chr2:114040000-114040800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
35	chr2:114040000-114041000	Weak transcription	Brain Germinal Matrix	brain
36	chr2:114040000-114041000	Weak transcription	Small Intestine	intestine
37	chr2:114040000-114041200	Enhancers	Spleen	Spleen
38	chr2:114040000-114041600	Flanking Active TSS	HepG2	liver
39	chr2:114040000-114042200	Enhancers	Sigmoid Colon	Sigmoid Colon
40	chr2:114040000-114042600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr2:114040200-114040600	Enhancers	Monocytes-CD14+_RO01746	blood
42	chr2:114040200-114041400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr2:114040200-114041600	Enhancers	Colonic Mucosa	Colon
44	chr2:114040200-114041800	Enhancers	Right Ventricle	heart
45	chr2:114040200-114042600	Enhancers	Primary monocytes fromperipheralblood	blood
46	chr2:114040400-114040600	Enhancers	Aorta	Aorta
47	chr2:114040400-114040600	Enhancers	Fetal Lung	lung
48	chr2:114040400-114040800	Flanking Active TSS	Duodenum Mucosa	Duodenum
49	chr2:114040400-114040800	Enhancers	Stomach Smooth Muscle	stomach
50	chr2:114040400-114040800	Enhancers	K562	blood

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