Variant report

Variant	rs11168838
Chromosome Location	chr12:49455006-49455007
allele	A/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	PRDM1	chr12:49454776-49455185	Hela-S3	cervix:	n/a	chr12:49454926-49454941
2	RUNX3	chr12:49453962-49455109	GM12878	blood:	n/a	n/a
3	WRNIP1	chr12:49454442-49455198	GM12878	blood:	n/a	n/a
4	MAX	chr12:49453904-49455216	HepG2	liver:	n/a	chr12:49454185-49454195 chr12:49454708-49454718 chr12:49454689-49454699 chr12:49454690-49454701
5	MYC	chr12:49454120-49455138	K562	blood:	n/a	chr12:49454185-49454195 chr12:49454708-49454718 chr12:49454689-49454699 chr12:49454690-49454701
6	POLR2A	chr12:49453789-49455394	K562	blood:	n/a	n/a
7	POLR2A	chr12:49453535-49455032	H1-hESC	embryonic stem cell:	n/a	n/a
8	CHD1	chr12:49451619-49455170	IMR90	lung:	n/a	chr12:49454043-49454053 chr12:49454374-49454384 chr12:49453842-49453852
9	MAX	chr12:49453645-49455144	HepG2	liver:	n/a	chr12:49454185-49454195 chr12:49454708-49454718 chr12:49454689-49454699 chr12:49454690-49454701
10	POLR2A	chr12:49452782-49455199	HUVEC	blood vessel:	n/a	n/a
11	TCF12	chr12:49453918-49455260	ECC-1	luminal epithelium:	n/a	n/a
12	POLR2A	chr12:49453533-49455168	HUVEC	blood vessel:	n/a	n/a
13	POLR2A	chr12:49453984-49455101	GM12878	blood:	n/a	n/a
14	MYC	chr12:49454150-49455080	Hela-S3	cervix:	n/a	chr12:49454185-49454195 chr12:49454708-49454718 chr12:49454689-49454699 chr12:49454690-49454701
15	TAF1	chr12:49454015-49455082	K562	blood:	n/a	n/a
16	MAX	chr12:49453436-49455228	ECC-1	luminal epithelium:	n/a	chr12:49454185-49454195 chr12:49454708-49454718 chr12:49454689-49454699 chr12:49453616-49453625 chr12:49454690-49454701
17	POLR2A	chr12:49453033-49455284	Hela-S3	cervix:	n/a	n/a
18	BCL3	chr12:49454053-49455212	A549	lung:	n/a	chr12:49454720-49454729 chr12:49454357-49454370 chr12:49454950-49454963 chr12:49454180-49454193 chr12:49454892-49454905 chr12:49454573-49454582 chr12:49454363-49454376
19	POLR2A	chr12:49453637-49455095	MCF-7	breast:	n/a	n/a
20	TBL1XR1	chr12:49454438-49455106	K562	blood:	n/a	n/a
21	ZNF143	chr12:49454228-49455097	K562	blood:	n/a	chr12:49454271-49454289 chr12:49454899-49454918 chr12:49454370-49454388 chr12:49454904-49454922
22	HDAC2	chr12:49454134-49455204	MCF-7	breast:	n/a	n/a
23	ZBTB7A	chr12:49453691-49455037	K562	blood:	n/a	chr12:49454089-49454096
24	MTA3	chr12:49452741-49455410	GM12878	blood:	n/a	n/a
25	POLR2A	chr12:49453336-49455117	GM18951	blood:	n/a	n/a
26	MAFK	chr12:49454427-49455089	Hela-S3	cervix:	n/a	n/a
27	MAFK	chr12:49454300-49455057	K562	blood:	n/a	n/a
28	ATF2	chr12:49454237-49455154	H1-hESC	embryonic stem cell:	n/a	n/a
29	SIX5	chr12:49454447-49455093	GM12878	blood:	n/a	n/a
30	ATF2	chr12:49454425-49455036	H1-hESC	embryonic stem cell:	n/a	n/a
31	MYC	chr12:49453954-49455492	K562	blood:	n/a	chr12:49454185-49454195 chr12:49454708-49454718 chr12:49454689-49454699 chr12:49454690-49454701
32	KAP1	chr12:49454315-49455168	HEK293	kidney:	n/a	n/a
33	POLR2A	chr12:49453932-49455079	U87	brain:	n/a	n/a
34	POLR2A	chr12:49454111-49455134	SK-N-MC	brain:	n/a	n/a
35	CREB1	chr12:49454114-49455112	HepG2	liver:	n/a	n/a
36	JUND	chr12:49453566-49455155	A549	lung:	n/a	chr12:49454115-49454124 chr12:49453840-49453849
37	ELF1	chr12:49453481-49455109	GM12878	blood:	n/a	chr12:49454278-49454290
38	POLR2A	chr12:49453927-49455028	PANC-1	pancreas:	n/a	n/a
39	YY1	chr12:49453953-49455039	HCT-116	colon:	n/a	chr12:49454382-49454391 chr12:49454180-49454189 chr12:49454721-49454730
40	POLR2A	chr12:49453586-49455210	GM12891	blood:	n/a	n/a
41	PAX5	chr12:49454292-49455048	GM12878	blood:	n/a	n/a
42	MAX	chr12:49454432-49455125	A549	lung:	n/a	chr12:49454708-49454718 chr12:49454689-49454699 chr12:49454690-49454701
43	ZNF143	chr12:49454117-49455097	GM12878	blood:	n/a	chr12:49454271-49454289 chr12:49454899-49454918 chr12:49454370-49454388 chr12:49454904-49454922
44	TBP	chr12:49454103-49455155	Hela-S3	cervix:	n/a	n/a
45	TCF12	chr12:49453092-49455328	ECC-1	luminal epithelium:	n/a	n/a
46	ZKSCAN1	chr12:49454297-49455070	Hela-S3	cervix:	n/a	n/a
47	PBX3	chr12:49454062-49455063	A549	lung:	n/a	n/a
48	CREB1	chr12:49453843-49455189	HepG2	liver:	n/a	n/a
49	MAZ	chr12:49452677-49455391	IMR90	lung:	n/a	chr12:49454185-49454195 chr12:49454708-49454718 chr12:49453616-49453625 chr12:49454690-49454701
50	E2F6	chr12:49454232-49455041	H1-hESC	embryonic stem cell:	n/a	chr12:49454757-49454766 chr12:49454368-49454377

No.	Distal block	Cell Line	Cell type
1	chr12:49447251..49459518-chr12:49480338..49487981,17	K562	blood:
2	chr12:49446392..49469923-chr12:49518127..49527853,66	K562	blood:
3	chr12:49454044..49455042-chr7:74489029..74489605,2	Hela-S3	cervix:
4	chr12:49454563..49455155-chr7:87848985..87849619,2	Hela-S3	cervix:
5	chr12:49452282..49457106-chr12:49501761..49505806,6	K562	blood:
6	chr12:49454519..49456146-chr12:49518450..49520745,2	MCF-7	breast:
7	chr12:49408338..49419708-chr12:49447252..49460551,38	K562	blood:
8	chr12:49453309..49455961-chr12:49948897..49951747,2	MCF-7	breast:
9	chr12:49453115..49455291-chr12:49657846..49660975,4	MCF-7	breast:
10	chr12:49454021..49456179-chr12:49508366..49510938,2	K562	blood:
11	chr12:49452588..49458658-chr12:49486666..49491439,6	MCF-7	breast:
12	chr12:49448896..49462070-chr12:49656751..49663992,28	K562	blood:
13	chr12:49451508..49465481-chr12:49521303..49528986,40	MCF-7	breast:
14	chr12:49454631..49456849-chr12:49504734..49506537,2	K562	blood:
15	chr12:49454377..49456128-chr12:49555146..49557266,2	K562	blood:
16	chr12:49409714..49416851-chr12:49447402..49455499,24	MCF-7	breast:
17	chr12:49450455..49459531-chr12:49522374..49527837,16	MCF-7	breast:
18	chr12:49454627..49456339-chr12:49470882..49473684,2	K562	blood:
19	chr12:49440399..49469923-chr12:49518291..49528303,83	K562	blood:
20	chr12:49365267..49367565-chr12:49453514..49456197,2	K562	blood:
21	chr12:49454177..49455905-chr12:49464920..49466529,2	MCF-7	breast:
22	chr12:49454829..49457551-chr12:49626042..49628267,3	K562	blood:
23	chr12:49453076..49457977-chr12:49485062..49491403,12	K562	blood:
24	chr12:46765603..46767339-chr12:49452531..49455344,2	K562	blood:
25	chr12:49450480..49457103-chr12:49487982..49492074,8	K562	blood:
26	chr12:49453688..49456279-chr12:49494326..49496673,3	K562	blood:
27	chr12:49418054..49419744-chr12:49454256..49456208,2	MCF-7	breast:
28	chr12:49452850..49457008-chr12:49658832..49661007,5	MCF-7	breast:
29	chr10:14920093..14920668-chr12:49454106..49455063,2	Hela-S3	cervix:
30	chr12:49211350..49214001-chr12:49453993..49456972,2	MCF-7	breast:
31	chr12:49407466..49416688-chr12:49451532..49456163,12	MCF-7	breast:
32	chr12:49449335..49458365-chr12:49656751..49666981,25	K562	blood:

Variant related genes	Relation type
KMT2D	TF binding region
ENSG00000181929	Chromatin interaction
ENSG00000200309	Chromatin interaction
ENSG00000169884	Chromatin interaction
ENSG00000167553	Chromatin interaction
ENSG00000075142	Chromatin interaction
ENSG00000258101	Chromatin interaction
ENSG00000257346	Chromatin interaction
ENSG00000167535	Chromatin interaction
ENSG00000258017	Chromatin interaction
ENSG00000134294	Chromatin interaction
ENSG00000139636	Chromatin interaction
ENSG00000135519	Chromatin interaction
ENSG00000139549	Chromatin interaction
ENSG00000167548	Chromatin interaction
ENSG00000123416	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10459221	0.94[ASN][1000 genomes]
rs10459232	0.94[ASN][1000 genomes]
rs1054442	0.80[ASN][1000 genomes]
rs10783300	0.83[ASN][1000 genomes]
rs10783301	0.92[ASN][1000 genomes]
rs10875908	0.83[ASN][1000 genomes]
rs10875910	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10875911	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10875912	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10875913	0.86[ASN][1000 genomes]
rs10875914	0.87[ASN][1000 genomes]
rs10875915	0.87[ASN][1000 genomes]
rs10875917	0.94[ASN][1000 genomes]
rs10875918	0.94[ASN][1000 genomes]
rs11168822	0.81[ASN][1000 genomes]
rs11168827	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11168839	0.99[ASN][1000 genomes]
rs11168850	0.94[ASN][1000 genomes]
rs1138908	0.83[ASN][1000 genomes]
rs11614738	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12298884	0.90[ASN][1000 genomes]
rs12580349	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12821008	0.94[ASN][1000 genomes]
rs2117029	0.83[ASN][1000 genomes]
rs2241726	0.92[ASN][1000 genomes]
rs2293445	0.83[ASN][1000 genomes]
rs2293446	0.84[ASN][1000 genomes]
rs2304275	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs34436857	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3741622	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3782357	0.87[ASN][1000 genomes]
rs6580698	0.91[ASN][1000 genomes]
rs6580699	0.91[ASN][1000 genomes]
rs7296288	0.89[ASN][1000 genomes]
rs7300136	0.94[ASN][1000 genomes]
rs7969091	0.99[ASN][1000 genomes]
rs876333	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832404	chr12:49258560-49458555	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
4	nsv558833	chr12:49358880-49478812	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
5	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases
6	esv3360842	chr12:49452910-49455458	Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11168838	RP11-386G11.5	cis	Muscle Skeletal	GTEx
rs11168838	DDN	cis	Muscle Skeletal	GTEx
rs11168838	RP11-386G11.3	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49450200-49455200	Active TSS	HSMMtube	muscle
2	chr12:49450800-49455400	Active TSS	Fetal Kidney	kidney
3	chr12:49451200-49455200	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr12:49451400-49455200	Active TSS	Lung	lung
5	chr12:49451800-49455200	Active TSS	HSMM	muscle
6	chr12:49451800-49455600	Active TSS	NHDF-Ad	bronchial
7	chr12:49452000-49455200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr12:49452000-49455200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr12:49452000-49455200	Active TSS	Psoas Muscle	Psoas
10	chr12:49452000-49455200	Bivalent/Poised TSS	HepG2	liver
11	chr12:49452000-49455400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr12:49452000-49455400	Active TSS	Esophagus	oesophagus
13	chr12:49452200-49455400	Active TSS	Aorta	Aorta
14	chr12:49452400-49455200	Active TSS	Gastric	stomach
15	chr12:49452400-49455200	Active TSS	Small Intestine	intestine
16	chr12:49452400-49455200	Active TSS	A549	lung
17	chr12:49452400-49455400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr12:49452400-49455400	Active TSS	H9 Cell Line	embryonic stem cell
19	chr12:49452400-49455400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr12:49452400-49455600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr12:49452600-49455200	Active TSS	HUES6 Cell Line	embryonic stem cell
22	chr12:49452600-49455400	Active TSS	Rectal Smooth Muscle	rectum
23	chr12:49452600-49455400	Active TSS	HMEC	breast
24	chr12:49452800-49455200	Active TSS	HUES64 Cell Line	embryonic stem cell
25	chr12:49452800-49455200	Active TSS	iPS-15b Cell Line	embryonic stem cell
26	chr12:49452800-49455200	Active TSS	iPS-20b Cell Line	embryonic stem cell
27	chr12:49452800-49455200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr12:49452800-49455200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr12:49452800-49455200	Active TSS	Ovary	ovary
30	chr12:49452800-49455400	Active TSS	Colon Smooth Muscle	Colon
31	chr12:49452800-49455400	Active TSS	Left Ventricle	heart
32	chr12:49452800-49455400	Active TSS	Hela-S3	cervix
33	chr12:49452800-49455400	Active TSS	NHLF	lung
34	chr12:49452800-49455600	Active TSS	ES-I3 Cell Line	embryonic stem cell
35	chr12:49453000-49455200	Active TSS	Brain Substantia Nigra	brain
36	chr12:49453000-49455200	Active TSS	Duodenum Smooth Muscle	Duodenum
37	chr12:49453000-49455400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr12:49453200-49455400	Active TSS	K562	blood
39	chr12:49453200-49455600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr12:49453400-49455200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
41	chr12:49453400-49455200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr12:49453400-49455200	Active TSS	Placenta	Placenta
43	chr12:49453400-49455400	Active TSS	H1 Cell Line	embryonic stem cell
44	chr12:49453400-49455400	Active TSS	Right Ventricle	heart
45	chr12:49453600-49455200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr12:49453600-49455400	Active TSS	Colonic Mucosa	Colon
47	chr12:49454200-49455200	Transcr. at gene 5' and 3'	Right Atrium	heart
48	chr12:49454200-49455400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr12:49454200-49455600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr12:49454400-49455200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin

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