Variant report

Variant	rs11042365
Chromosome Location	chr11:9481601-9481602
allele	C/G
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	POLR2A	chr11:9480308-9483702	PFSK-1	brain:	n/a	n/a
2	SIN3AK20	chr11:9481457-9481814	A549	lung:	n/a	n/a
3	TAF1	chr11:9481378-9483190	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr11:9480817-9484127	GM18505	blood:	n/a	n/a
5	CHD2	chr11:9481133-9483012	K562	blood:	n/a	chr11:9482147-9482157
6	SP1	chr11:9481262-9483289	HCT-116	colon:	n/a	chr11:9482284-9482293 chr11:9482494-9482515 chr11:9482368-9482377 chr11:9482511-9482520 chr11:9482509-9482521 chr11:9482366-9482377 chr11:9482450-9482471 chr11:9482510-9482519 chr11:9482509-9482521
7	POLR2A	chr11:9480875-9483890	U87	brain:	n/a	n/a
8	POLR2A	chr11:9481042-9483691	HL-60	blood:	n/a	n/a
9	TEAD4	chr11:9481277-9483422	K562	blood:	n/a	n/a
10	NFIC	chr11:9481586-9482416	ECC-1	luminal epithelium:	n/a	n/a
11	TBP	chr11:9481249-9483906	Hela-S3	cervix:	n/a	n/a
12	FOXM1	chr11:9481183-9483652	GM12878	blood:	n/a	n/a
13	POLR2A	chr11:9481141-9483836	GM18951	blood:	n/a	n/a
14	TAF1	chr11:9481273-9482320	SK-N-SH	brain:	n/a	n/a
15	MXI1	chr11:9481565-9483184	HepG2	liver:	n/a	chr11:9481818-9481833
16	TBL1XR1	chr11:9481171-9483236	GM12878	blood:	n/a	n/a
17	HEY1	chr11:9481012-9482322	HepG2	liver:	n/a	n/a
18	POLR2A	chr11:9480878-9483810	HCT-116	colon:	n/a	n/a
19	POLR2A	chr11:9481144-9483699	ProgFib	skin:	n/a	n/a
20	MYC	chr11:9481383-9483217	H1-hESC	embryonic stem cell:	n/a	n/a
21	ATF2	chr11:9481264-9483210	GM12878	blood:	n/a	chr11:9482393-9482404
22	POLR2A	chr11:9480642-9483619	K562	blood:	n/a	n/a
23	POLR2A	chr11:9480568-9483216	ECC-1	luminal epithelium:	n/a	n/a
24	POLR2A	chr11:9481003-9483224	HEK293	kidney:	n/a	n/a
25	SIN3AK20	chr11:9481323-9483178	PANC-1	pancreas:	n/a	n/a
26	MAX	chr11:9481578-9483249	GM12878	blood:	n/a	n/a
27	POLR2A	chr11:9481115-9483344	GM12891	blood:	n/a	n/a
28	HCFC1	chr11:9481567-9483258	K562	blood:	n/a	n/a
29	POLR2A	chr11:9481131-9483713	HUVEC	blood vessel:	n/a	n/a
30	POLR2A	chr11:9480818-9483893	PFSK-1	brain:	n/a	n/a
31	POLR2A	chr11:9481321-9483201	H1-hESC	embryonic stem cell:	n/a	n/a
32	TAF1	chr11:9481531-9483207	K562	blood:	n/a	n/a
33	CUX1	chr11:9481497-9482262	K562	blood:	n/a	n/a
34	RELA	chr11:9481371-9483245	GM12891	blood:	n/a	n/a
35	YY1	chr11:9481330-9483187	GM12878	blood:	n/a	chr11:9482220-9482242 chr11:9482686-9482700 chr11:9482769-9482783 chr11:9482689-9482703 chr11:9482671-9482680 chr11:9483065-9483076 chr11:9482689-9482698 chr11:9482534-9482548 chr11:9482686-9482695 chr11:9482672-9482686 chr11:9482231-9482239
36	RUNX3	chr11:9481201-9483254	GM12878	blood:	n/a	chr11:9481765-9481774 chr11:9482532-9482547 chr11:9481591-9481600 chr11:9481765-9481774 chr11:9481591-9481608 chr11:9482412-9482429
37	CEBPB	chr11:9481068-9481621	K562	blood:	n/a	n/a
38	POLR2A	chr11:9481174-9483432	Hela-S3	cervix:	n/a	n/a
39	NFIC	chr11:9481315-9484131	GM12878	blood:	n/a	n/a
40	FOXM1	chr11:9481425-9483404	GM12878	blood:	n/a	n/a
41	POLR2A	chr11:9481415-9483217	HepG2	liver:	n/a	n/a
42	REST	chr11:9481019-9483943	H1-neurons	neurons:	n/a	chr11:9482673-9482686 chr11:9482938-9482951 chr11:9483091-9483104 chr11:9483077-9483090
43	RFX5	chr11:9481392-9483797	Hela-S3	cervix:	n/a	n/a
44	MAZ	chr11:9481298-9484039	IMR90	lung:	n/a	n/a
45	PML	chr11:9480975-9483622	K562	blood:	n/a	n/a
46	POLR2A	chr11:9479740-9484253	SK-N-MC	brain:	n/a	n/a
47	RUNX3	chr11:9481070-9483205	GM12878	blood:	n/a	chr11:9481765-9481774 chr11:9482532-9482547 chr11:9481591-9481600 chr11:9481765-9481774 chr11:9481591-9481608 chr11:9482412-9482429
48	ATF2	chr11:9481347-9483043	GM12878	blood:	n/a	chr11:9482393-9482404
49	REST	chr11:9481451-9481764	A549	lung:	n/a	n/a
50	PML	chr11:9481001-9483235	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:9481508..9485106-chr11:9595203..9601095,6	MCF-7	breast:
2	chr11:9480226..9484903-chr11:9591788..9598525,12	MCF-7	breast:
3	chr11:9481580..9482474-chr17:7387306..7388177,3	Hela-S3	cervix:
4	chr11:9333668..9337804-chr11:9478729..9484496,11	K562	blood:
5	chr11:9444949..9446836-chr11:9480853..9482944,2	K562	blood:
6	chr11:9465547..9467985-chr11:9478686..9481606,2	MCF-7	breast:
7	chr11:9481080..9484532-chr11:9545856..9548015,3	MCF-7	breast:
8	chr11:9285385..9287169-chr11:9480610..9482898,2	K562	blood:
9	chr11:9478618..9485582-chr11:9593299..9599536,13	K562	blood:
10	chr11:9285399..9287969-chr11:9480073..9484247,5	MCF-7	breast:
11	chr11:9284942..9289829-chr11:9481407..9484206,5	MCF-7	breast:
12	chr11:9429811..9433973-chr11:9481355..9484368,4	MCF-7	breast:
13	chr11:9481490..9482152-chr11:62608638..62609549,2	NB4	blood:
14	chr11:9405101..9410331-chr11:9478772..9485340,14	K562	blood:
15	chr11:9479692..9486524-chr11:9491765..9498081,14	K562	blood:
16	chr11:9334187..9337944-chr11:9481178..9484496,6	K562	blood:
17	chr11:9479099..9485582-chr11:9593306..9599058,18	K562	blood:
18	chr11:9403958..9411793-chr11:9477944..9485616,22	K562	blood:
19	chr11:9479980..9482925-chr11:9627285..9628824,2	MCF-7	breast:
20	chr11:9481460..9483596-chr11:9780067..9782132,2	K562	blood:
21	chr11:9481559..9482413-chr12:58165702..58166309,2	Hela-S3	cervix:
22	chr11:9285208..9288330-chr11:9480610..9483327,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TMEM41B-5	chr11:9481103-9482245	NONHSAT017922

Variant related genes	Relation type
ZNF143	TF binding region
ENSG00000184014	Chromatin interaction
ENSG00000166478	Chromatin interaction
ENSG00000166483	Chromatin interaction
ENSG00000205339	Chromatin interaction
ENSG00000245522	Chromatin interaction
ENSG00000037897	Chromatin interaction
ENSG00000174282	Chromatin interaction
ENSG00000166471	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000181222	Chromatin interaction
ENSG00000243964	Chromatin interaction
ENSG00000123427	Chromatin interaction
ENSG00000238387	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10082685	0.84[EUR][1000 genomes]
rs10128708	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10840246	0.91[EUR][1000 genomes]
rs11042323	0.85[AMR][1000 genomes]
rs11042324	0.92[AMR][1000 genomes]
rs11042325	0.92[AMR][1000 genomes]
rs11042346	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11042361	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11042363	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11042367	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11042379	0.94[EUR][1000 genomes]
rs11042401	0.80[EUR][1000 genomes]
rs11042402	0.81[EUR][1000 genomes]
rs11600357	0.81[EUR][1000 genomes]
rs11601068	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11602025	0.84[EUR][1000 genomes]
rs11602056	0.84[EUR][1000 genomes]
rs11607631	0.84[EUR][1000 genomes]
rs12272069	0.92[AMR][1000 genomes]
rs12274646	0.94[EUR][1000 genomes]
rs12276413	0.92[AMR][1000 genomes]
rs12279202	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12280032	0.84[EUR][1000 genomes]
rs12280301	0.84[EUR][1000 genomes]
rs12282862	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12284187	0.88[EUR][1000 genomes]
rs12285570	0.82[EUR][1000 genomes]
rs12286949	0.85[AMR][1000 genomes]
rs12292907	0.84[EUR][1000 genomes]
rs12293264	0.84[EUR][1000 genomes]
rs12293634	0.91[EUR][1000 genomes]
rs12294461	0.85[AMR][1000 genomes]
rs1546	0.84[EUR][1000 genomes]
rs16906804	0.92[AMR][1000 genomes]
rs28463550	0.92[AMR][1000 genomes]
rs34485398	0.85[AMR][1000 genomes]
rs36048375	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4910052	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4910463	0.85[AMR][1000 genomes]
rs4910466	0.84[EUR][1000 genomes]
rs4910467	0.84[EUR][1000 genomes]
rs4910469	0.81[EUR][1000 genomes]
rs4910471	0.80[EUR][1000 genomes]
rs55750964	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56116319	0.91[EUR][1000 genomes]
rs56320702	0.91[EUR][1000 genomes]
rs9988896	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916534	chr11:9188436-9516241	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv1055078	chr11:9252857-9538877	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv427882	chr11:9431600-9626580	Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
4	nsv1039537	chr11:9455387-9535970	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11042365	ZNF143	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9480600-9483800	Active TSS	Placenta	Placenta
2	chr11:9480600-9484000	Active TSS	iPS-18 Cell Line	embryonic stem cell
3	chr11:9480800-9481800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr11:9480800-9481800	Active TSS	Right Atrium	heart
5	chr11:9480800-9482800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr11:9480800-9483200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr11:9480800-9483400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr11:9480800-9483400	Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr11:9480800-9483400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr11:9480800-9483400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr11:9480800-9483400	Active TSS	Brain Cingulate Gyrus	brain
12	chr11:9480800-9483400	Active TSS	Rectal Smooth Muscle	rectum
13	chr11:9480800-9483400	Active TSS	HMEC	breast
14	chr11:9480800-9483400	Active TSS	NHEK	skin
15	chr11:9480800-9483600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr11:9480800-9483600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr11:9480800-9483600	Active TSS	Esophagus	oesophagus
18	chr11:9480800-9483600	Active TSS	Pancreas	Pancrea
19	chr11:9480800-9483800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr11:9480800-9483800	Active TSS	iPS-15b Cell Line	embryonic stem cell
21	chr11:9480800-9483800	Active TSS	GM12878-XiMat	blood
22	chr11:9480800-9484000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr11:9480800-9484000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr11:9480800-9484000	Active TSS	HUES6 Cell Line	embryonic stem cell
25	chr11:9480800-9484000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr11:9480800-9484000	Active TSS	Fetal Brain Female	brain
27	chr11:9480800-9484000	Active TSS	Skeletal Muscle Male	skeletal muscle
28	chr11:9480800-9484200	Active TSS	H1 Cell Line	embryonic stem cell
29	chr11:9480800-9484200	Active TSS	H9 Cell Line	embryonic stem cell
30	chr11:9480800-9484200	Active TSS	HUES48 Cell Line	embryonic stem cell
31	chr11:9480800-9484200	Active TSS	HUES64 Cell Line	embryonic stem cell
32	chr11:9480800-9484200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr11:9480800-9484200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr11:9480800-9484200	Active TSS	HSMM	muscle
35	chr11:9481000-9482000	Flanking Active TSS	Primary B cells from cord blood	blood
36	chr11:9481000-9482000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
37	chr11:9481000-9482200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
38	chr11:9481000-9483000	Active TSS	Primary hematopoietic stem cells	blood
39	chr11:9481000-9483200	Active TSS	Primary T cells from cord blood	blood
40	chr11:9481000-9483200	Active TSS	NH-A	brain
41	chr11:9481000-9483400	Active TSS	Brain Angular Gyrus	brain
42	chr11:9481000-9483400	Active TSS	Brain Anterior Caudate	brain
43	chr11:9481000-9483400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
44	chr11:9481000-9483400	Active TSS	Fetal Kidney	kidney
45	chr11:9481000-9483400	Active TSS	Stomach Smooth Muscle	stomach
46	chr11:9481000-9483400	Active TSS	A549	lung
47	chr11:9481000-9483600	Active TSS	Liver	Liver
48	chr11:9481000-9483600	Active TSS	Brain Inferior Temporal Lobe	brain
49	chr11:9481000-9483600	Active TSS	Fetal Stomach	stomach
50	chr11:9481000-9483600	Active TSS	Left Ventricle	heart

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