Variant report

Variant	rs11043218
Chromosome Location	chr12:122297277-122297278
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	TEAD4	chr12:122297223-122297560	H1-hESC	embryonic stem cell:	n/a	n/a
2	MAX	chr12:122296742-122297616	ECC-1	luminal epithelium:	n/a	n/a
3	TCF12	chr12:122296959-122297667	ECC-1	luminal epithelium:	n/a	n/a
4	ATF2	chr12:122297203-122297537	H1-hESC	embryonic stem cell:	n/a	n/a
5	SMARCC1	chr12:122296967-122297648	Hela-S3	cervix:	n/a	n/a
6	NR3C1	chr12:122297164-122297488	ECC-1	luminal epithelium:	n/a	n/a
7	HSF1	chr12:122296665-122297501	HepG2	liver:	n/a	chr12:122296859-122296874
8	POLR2A	chr12:122294436-122297491	HepG2	liver:	n/a	n/a
9	FOXA2	chr12:122296768-122297461	HepG2	liver:	n/a	n/a
10	FOSL2	chr12:122296750-122297612	HepG2	liver:	n/a	chr12:122297450-122297461
11	RCOR1	chr12:122296535-122297539	HepG2	liver:	n/a	n/a
12	EP300	chr12:122297242-122297502	Hela-S3	cervix:	n/a	n/a
13	KAP1	chr12:122297218-122297554	U2OS	brain:	n/a	n/a
14	SP1	chr12:122297115-122297618	H1-hESC	embryonic stem cell:	n/a	n/a
15	JUND	chr12:122297083-122297774	T-47D	breast:	n/a	chr12:122297450-122297461
16	CREB1	chr12:122296234-122297662	HepG2	liver:	n/a	n/a
17	MYC	chr12:122297258-122297390	HepG2	liver:	n/a	n/a
18	TEAD4	chr12:122297131-122297655	H1-hESC	embryonic stem cell:	n/a	n/a
19	MBD4	chr12:122296449-122297524	HepG2	liver:	n/a	n/a
20	NFIC	chr12:122296720-122297277	HepG2	liver:	n/a	n/a
21	MAZ	chr12:122296557-122297577	HepG2	liver:	n/a	n/a
22	GATA3	chr12:122297042-122297561	T-47D	breast:	n/a	n/a
23	ATF2	chr12:122297148-122297578	H1-hESC	embryonic stem cell:	n/a	n/a
24	JUND	chr12:122297005-122297639	SK-N-SH	brain:	n/a	chr12:122297450-122297461
25	FOS	chr12:122297239-122297575	MCF10A-Er-Src	breast:	n/a	chr12:122297450-122297461
26	CEBPB	chr12:122297087-122297551	IMR90	lung:	n/a	n/a
27	HNF4A	chr12:122296502-122297515	HepG2	liver:	n/a	chr12:122297037-122297052 chr12:122297388-122297403 chr12:122296532-122296547
28	HNF4G	chr12:122296695-122297317	HepG2	liver:	n/a	chr12:122297036-122297051
29	CREB1	chr12:122297277-122297517	A549	lung:	n/a	n/a
30	HDAC2	chr12:122296594-122297506	HepG2	liver:	n/a	chr12:122296621-122296635 chr12:122296626-122296640
31	TEAD4	chr12:122296770-122297581	SK-N-SH	brain:	n/a	n/a
32	NFIC	chr12:122296681-122297662	ECC-1	luminal epithelium:	n/a	n/a
33	POLR2A	chr12:122296333-122297450	HepG2	liver:	n/a	n/a
34	NR3C1	chr12:122297143-122297522	ECC-1	luminal epithelium:	n/a	n/a
35	FOS	chr12:122297240-122297565	MCF10A-Er-Src	breast:	n/a	chr12:122297450-122297461
36	JUND	chr12:122297180-122297494	A549	lung:	n/a	chr12:122297450-122297461
37	JUN	chr12:122297212-122297569	Hela-S3	cervix:	n/a	chr12:122297390-122297403 chr12:122297450-122297461
38	SIN3AK20	chr12:122297253-122297457	SK-N-SH	brain:	n/a	n/a
39	ATF3	chr12:122297236-122297495	HepG2	liver:	n/a	n/a
40	JUN	chr12:122297002-122297619	HepG2	liver:	n/a	chr12:122297390-122297403 chr12:122297450-122297461
41	NFIC	chr12:122296623-122297729	SK-N-SH	brain:	n/a	n/a
42	MAX	chr12:122296829-122297538	Hela-S3	cervix:	n/a	n/a
43	JUND	chr12:122296766-122297715	SK-N-SH	brain:	n/a	chr12:122297450-122297461
44	JUND	chr12:122297141-122297613	H1-hESC	embryonic stem cell:	n/a	chr12:122297450-122297461
45	POLR2A	chr12:122297111-122297561	SK-N-SH	brain:	n/a	n/a
46	ARID3A	chr12:122296705-122297646	HepG2	liver:	n/a	n/a
47	MYBL2	chr12:122296395-122297723	HepG2	liver:	n/a	n/a
48	MBD4	chr12:122296827-122297548	HepG2	liver:	n/a	n/a
49	JUN	chr12:122297184-122297548	H1-hESC	embryonic stem cell:	n/a	chr12:122297390-122297403 chr12:122297450-122297461
50	EP300	chr12:122296681-122297517	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:122297229..122298765-chr12:122371936..122374229,2	K562	blood:
2	chr12:122231575..122234439-chr12:122297036..122301100,4	MCF-7	breast:
3	chr12:122240928..122242947-chr12:122294701..122297543,2	MCF-7	breast:

Variant related genes	Relation type
HPD	TF binding region
ENSG00000158023	Chromatin interaction
ENSG00000139725	Chromatin interaction
ENSG00000212694	Chromatin interaction
ENSG00000139718	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10840622	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10840624	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11043213	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11043216	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11043217	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11043219	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11043220	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs11043223	0.96[CEU][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs11043225	0.92[EUR][1000 genomes]
rs11043229	0.91[CHB][hapmap]
rs11043237	0.91[CHB][hapmap]
rs11043242	0.81[CHB][hapmap]
rs12825161	0.91[EUR][1000 genomes]
rs1610041	0.85[CEU][hapmap];0.91[CHB][hapmap];0.94[MEX][hapmap];0.82[TSI][hapmap];0.88[YRI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2167067	0.93[EUR][1000 genomes]
rs35599566	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35633723	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35892692	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3847694	0.91[CHB][hapmap];0.88[GIH][hapmap];0.83[TSI][hapmap]
rs6486780	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs66611928	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs68055743	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7137218	0.92[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.85[TSI][hapmap]
rs7137708	1.00[JPT][hapmap]
rs7313252	0.91[CHB][hapmap]
rs7958406	0.90[CHB][hapmap]
rs7969671	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][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	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	nsv916686	chr12:122240149-122714056	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv899568	chr12:122254713-122456524	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11043218	LOC338799	cis	parietal	SCAN
rs11043218	HPD	cis	Muscle Skeletal	GTEx
rs11043218	DIABLO	cis	parietal	SCAN
rs11043218	HPD	cis	Heart Left Ventricle	GTEx
rs11043218	OASL	cis	parietal	SCAN
rs11043218	WDR66	cis	cerebellum	SCAN
rs11043218	RP11-7M8.2	cis	Muscle Skeletal	GTEx

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122294000-122298600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:122294200-122297600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr12:122294200-122297800	Weak transcription	Primary B cells from cord blood	blood
4	chr12:122294200-122299000	Enhancers	A549	lung
5	chr12:122294600-122297800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:122294800-122298800	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr12:122295200-122298600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr12:122295400-122297400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:122295400-122297400	Enhancers	Pancreas	Pancrea
10	chr12:122295400-122297800	Enhancers	Fetal Intestine Small	intestine
11	chr12:122295400-122300000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr12:122295400-122300400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr12:122295600-122298000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr12:122295600-122298400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr12:122295600-122298400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr12:122295600-122298400	Enhancers	Adipose Nuclei	Adipose
17	chr12:122295600-122298600	Enhancers	H1 Cell Line	embryonic stem cell
18	chr12:122295600-122298600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr12:122295800-122297600	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr12:122295800-122297600	Enhancers	Osteobl	bone
21	chr12:122295800-122299200	Weak transcription	K562	blood
22	chr12:122296200-122298000	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr12:122296200-122298400	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr12:122296200-122298800	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr12:122296400-122297400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr12:122296400-122297600	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr12:122296400-122297800	Enhancers	Colonic Mucosa	Colon
28	chr12:122296400-122297800	Enhancers	Fetal Muscle Leg	muscle
29	chr12:122296400-122297800	Enhancers	Fetal Stomach	stomach
30	chr12:122296400-122297800	Enhancers	Ovary	ovary
31	chr12:122296400-122297800	Enhancers	Right Ventricle	heart
32	chr12:122296400-122297800	Enhancers	HSMM	muscle
33	chr12:122296400-122297800	Enhancers	HSMMtube	muscle
34	chr12:122296400-122298000	Enhancers	NHLF	lung
35	chr12:122296400-122298400	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr12:122296400-122298400	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr12:122296400-122298600	Enhancers	Right Atrium	heart
38	chr12:122296400-122298600	Enhancers	Hela-S3	cervix
39	chr12:122296600-122297400	Enhancers	Placenta	Placenta
40	chr12:122296600-122297600	Enhancers	HUES48 Cell Line	embryonic stem cell
41	chr12:122296600-122297600	Enhancers	HUES64 Cell Line	embryonic stem cell
42	chr12:122296600-122297600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr12:122296600-122297600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr12:122296600-122297600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr12:122296600-122297600	Enhancers	Fetal Heart	heart
46	chr12:122296600-122297600	Enhancers	NH-A	brain
47	chr12:122296600-122297600	Enhancers	NHDF-Ad	bronchial
48	chr12:122296600-122297800	Enhancers	Rectal Mucosa Donor 31	rectum
49	chr12:122296600-122297800	Flanking Active TSS	Stomach Smooth Muscle	stomach
50	chr12:122296600-122298000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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