Variant report

Variant	rs11168536
Chromosome Location	chr12:48745051-48745052
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	MAX	chr12:48744264-48745384	K562	blood:	n/a	n/a
2	CHD2	chr12:48743920-48745171	GM12878	blood:	n/a	n/a
3	TCF7L2	chr12:48744071-48745162	HCT-116	colon:	n/a	n/a
4	TAF1	chr12:48744838-48745193	Hela-S3	cervix:	n/a	n/a
5	CUX1	chr12:48744909-48745244	K562	blood:	n/a	n/a
6	ZNF143	chr12:48744921-48745280	K562	blood:	n/a	chr12:48744933-48744943
7	GATA3	chr12:48744834-48745309	T-47D	breast:	n/a	n/a
8	POLR2A	chr12:48744820-48745078	HepG2	liver:	n/a	n/a
9	RAD21	chr12:48744906-48745301	Hela-S3	cervix:	n/a	n/a
10	CEBPB	chr12:48744031-48745673	Hela-S3	cervix:	n/a	chr12:48745057-48745066 chr12:48745057-48745066 chr12:48745057-48745066 chr12:48745055-48745066
11	EP300	chr12:48744236-48745241	SK-N-SH	brain:	n/a	chr12:48744745-48744761 chr12:48744492-48744508 chr12:48744884-48744893 chr12:48744889-48744905 chr12:48744933-48744942
12	CTCF	chr12:48744940-48745090	HCPEpiC	choroid plexus:	n/a	n/a
13	TBL1XR1	chr12:48744867-48745615	K562	blood:	n/a	n/a
14	MAX	chr12:48743927-48745480	ECC-1	luminal epithelium:	n/a	chr12:48744116-48744126
15	TBP	chr12:48744199-48745295	K562	blood:	n/a	n/a
16	E2F4	chr12:48744607-48745098	MCF10A-Er-Src	breast:	n/a	chr12:48744610-48744620 chr12:48744929-48744938 chr12:48744884-48744893 chr12:48744732-48744741
17	JUND	chr12:48744229-48745369	K562	blood:	n/a	n/a
18	CEBPD	chr12:48744530-48745334	K562	blood:	n/a	chr12:48745057-48745066 chr12:48745056-48745067 chr12:48745056-48745067
19	POLR2A	chr12:48744139-48745058	MCF-7	breast:	n/a	n/a
20	TAF1	chr12:48744850-48745273	K562	blood:	n/a	n/a
21	YY1	chr12:48744364-48745101	K562	blood:	n/a	chr12:48744608-48744617 chr12:48744929-48744943 chr12:48744754-48744765 chr12:48744612-48744623 chr12:48744625-48744634 chr12:48744929-48744938
22	ATF1	chr12:48744934-48745258	K562	blood:	n/a	n/a
23	POLR2A	chr12:48744273-48745149	GM15510	blood:	n/a	n/a
24	TAF1	chr12:48743935-48745219	ECC-1	luminal epithelium:	n/a	n/a
25	CTCF	chr12:48744920-48745070	K562	blood:	n/a	n/a
26	JUND	chr12:48744970-48745157	HepG2	liver:	n/a	n/a
27	FOS	chr12:48745025-48745194	MCF10A-Er-Src	breast:	n/a	n/a
28	POLR2A	chr12:48744255-48745322	K562	blood:	n/a	n/a
29	POLR2A	chr12:48744147-48745291	IMR90	lung:	n/a	n/a
30	STAT3	chr12:48744863-48745170	MCF10A-Er-Src	breast:	n/a	n/a
31	POLR2A	chr12:48744371-48745329	K562	blood:	n/a	n/a
32	MAZ	chr12:48744178-48745233	HepG2	liver:	n/a	n/a
33	POLR2A	chr12:48744214-48745335	HL-60	blood:	n/a	n/a
34	CEBPB	chr12:48744864-48745249	HepG2	liver:	n/a	chr12:48745057-48745066 chr12:48745057-48745066 chr12:48745057-48745066 chr12:48745055-48745066
35	POLR2A	chr12:48744247-48745082	GM12878	blood:	n/a	n/a
36	E2F6	chr12:48744787-48745071	K562	blood:	n/a	chr12:48744929-48744938 chr12:48744884-48744893
37	POLR2A	chr12:48744019-48745190	ECC-1	luminal epithelium:	n/a	n/a
38	RCOR1	chr12:48744022-48745333	Hela-S3	cervix:	n/a	n/a
39	CEBPB	chr12:48744829-48745379	A549	lung:	n/a	chr12:48745057-48745066 chr12:48745057-48745066 chr12:48745057-48745066 chr12:48745055-48745066
40	TAF1	chr12:48744838-48745144	K562	blood:	n/a	n/a
41	HDAC2	chr12:48744846-48745125	H1-hESC	embryonic stem cell:	n/a	n/a
42	MTA3	chr12:48744809-48745343	GM12878	blood:	n/a	n/a
43	USF2	chr12:48744887-48745362	Hela-S3	cervix:	n/a	n/a
44	TEAD4	chr12:48744006-48745360	ECC-1	luminal epithelium:	n/a	n/a
45	ZMIZ1	chr12:48744936-48745285	K562	blood:	n/a	n/a
46	POLR2A	chr12:48744065-48745387	Hela-S3	cervix:	n/a	n/a
47	POLR2A	chr12:48744866-48745122	H1-hESC	embryonic stem cell:	n/a	n/a
48	CEBPB	chr12:48744838-48745604	A549	lung:	n/a	chr12:48745057-48745066 chr12:48745057-48745066 chr12:48745057-48745066 chr12:48745055-48745066
49	CEBPB	chr12:48744897-48745218	K562	blood:	n/a	chr12:48745057-48745066 chr12:48745057-48745066 chr12:48745057-48745066 chr12:48745055-48745066
50	POLR2A	chr12:48744070-48745243	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:62609046..62609646-chr12:48744563..48745096,2	Hela-S3	cervix:
2	chr11:114167108..114168028-chr12:48744737..48745376,2	Hela-S3	cervix:
3	chr12:48743746..48745739-chr15:100880509..100882154,2	MCF-7	breast:
4	chr12:48743811..48746136-chr12:49207748..49210431,2	MCF-7	breast:
5	chr12:48744164..48745071-chr20:32581340..32582207,2	Hela-S3	cervix:
6	chr12:48745029..48745711-chr5:68513355..68514024,2	Hela-S3	cervix:
7	chr12:48740296..48746434-chr12:48748194..48754526,9	MCF-7	breast:
8	chr12:48737402..48739098-chr12:48743829..48745442,2	MCF-7	breast:
9	chr1:11967957..11968603-chr12:48744529..48745285,2	Hela-S3	cervix:
10	chr12:48744030..48746480-chr12:48749780..48752086,4	K562	blood:
11	chr11:62608631..62609620-chr12:48744634..48745202,2	HCT-116	colon:
12	chr12:48741301..48746348-chr12:48747901..48753728,9	MCF-7	breast:
13	chr12:48743415..48745587-chr12:48758145..48761066,2	MCF-7	breast:
14	chr12:48727374..48736715-chr12:48738720..48747602,13	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-H1FNT-1	chr12:48745031-48746610	NONHSAT027996

Variant related genes	Relation type
ZNF641	TF binding region
ENSG00000258273	Chromatin interaction
ENSG00000269282	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000199347	Chromatin interaction
ENSG00000140470	Chromatin interaction
ENSG00000166741	Chromatin interaction
ENSG00000167535	Chromatin interaction
ENSG00000228265	Chromatin interaction
ENSG00000134056	Chromatin interaction
ENSG00000257763	Chromatin interaction
ENSG00000167528	Chromatin interaction
ENSG00000125970	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1021313	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10431526	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10437919	0.80[ASN][1000 genomes]
rs10437920	0.80[ASN][1000 genomes]
rs10467101	0.81[EUR][1000 genomes]
rs10875772	0.81[EUR][1000 genomes]
rs10875777	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10875778	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10875779	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10875792	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10875793	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10875799	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168487	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11168493	0.83[ASN][1000 genomes]
rs11168508	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11168510	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11168514	0.87[ASN][1000 genomes]
rs11168516	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11168520	0.95[ASN][1000 genomes]
rs12227601	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12313745	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12317751	0.80[ASN][1000 genomes]
rs12322347	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12322348	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1471997	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2054903	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2054904	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2279464	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2450992	0.93[ASN][1000 genomes]
rs2634675	0.95[ASN][1000 genomes]
rs2732439	0.95[ASN][1000 genomes]
rs2732465	0.95[ASN][1000 genomes]
rs2898065	0.83[EUR][1000 genomes]
rs3185921	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3751273	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4760625	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61941003	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61941006	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs716553	0.80[ASN][1000 genomes]
rs7297298	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7303055	0.80[ASN][1000 genomes]
rs7486008	0.80[ASN][1000 genomes]
rs9634261	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9788082	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv8971	chr12:48536526-48758501	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	esv34439	chr12:48541757-48779562	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	esv2757502	chr12:48547128-48779562	Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	nsv427911	chr12:48670336-48979396	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
7	nsv832402	chr12:48686761-48851020	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
8	nsv826362	chr12:48693048-48768853	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
9	nsv1045159	chr12:48730024-48748940	Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11168536	ZNF641	cis	Thyroid	GTEx
rs11168536	ZNF641	cis	Muscle Skeletal	GTEx
rs11168536	RP1-228P16.1	cis	Adipose Subcutaneous	GTEx
rs11168536	RP1-228P16.1	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48743000-48745600	Active TSS	Brain Inferior Temporal Lobe	brain
2	chr12:48743200-48745400	Active TSS	Ovary	ovary
3	chr12:48743200-48745600	Active TSS	Right Atrium	heart
4	chr12:48743400-48745200	Active TSS	GM12878-XiMat	blood
5	chr12:48743600-48745200	Active TSS	Fetal Muscle Trunk	muscle
6	chr12:48743600-48745200	Active TSS	HSMMtube	muscle
7	chr12:48743600-48745400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr12:48743600-48745400	Active TSS	Colonic Mucosa	Colon
9	chr12:48743600-48745400	Active TSS	Left Ventricle	heart
10	chr12:48743800-48745200	Active TSS	Small Intestine	intestine
11	chr12:48743800-48745200	Active TSS	NH-A	brain
12	chr12:48743800-48745400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr12:48743800-48745400	Active TSS	Esophagus	oesophagus
14	chr12:48743800-48745400	Active TSS	Gastric	stomach
15	chr12:48743800-48745600	Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr12:48743800-48745600	Active TSS	Colon Smooth Muscle	Colon
17	chr12:48744000-48745200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr12:48744000-48745200	Active TSS	HUES64 Cell Line	embryonic stem cell
19	chr12:48744000-48745200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr12:48744000-48745200	Active TSS	Primary T cells from cord blood	blood
21	chr12:48744000-48745200	Active TSS	Fetal Intestine Small	intestine
22	chr12:48744000-48745200	Active TSS	Placenta Amnion	Placenta Amnion
23	chr12:48744000-48745200	Active TSS	Sigmoid Colon	Sigmoid Colon
24	chr12:48744000-48745400	Active TSS	H1 Cell Line	embryonic stem cell
25	chr12:48744000-48745400	Active TSS	H9 Cell Line	embryonic stem cell
26	chr12:48744000-48745400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr12:48744000-48745400	Active TSS	iPS-15b Cell Line	embryonic stem cell
28	chr12:48744000-48745400	Active TSS	iPS-20b Cell Line	embryonic stem cell
29	chr12:48744000-48745400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr12:48744000-48745400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr12:48744000-48745400	Active TSS	Duodenum Smooth Muscle	Duodenum
32	chr12:48744000-48745400	Active TSS	Right Ventricle	heart
33	chr12:48744000-48745400	Active TSS	Stomach Mucosa	stomach
34	chr12:48744000-48745400	Active TSS	HSMM	muscle
35	chr12:48744000-48745600	Active TSS	Breast Myoepithelial Primary Cells	Breast
36	chr12:48744000-48745600	Active TSS	Aorta	Aorta
37	chr12:48744000-48745600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr12:48744000-48745600	Active TSS	Brain Substantia Nigra	brain
39	chr12:48744000-48745600	Active TSS	HepG2	liver
40	chr12:48744000-48745600	Active TSS	NHDF-Ad	bronchial
41	chr12:48744000-48745800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr12:48744000-48745800	Active TSS	Brain Cingulate Gyrus	brain
43	chr12:48744000-48745800	Active TSS	Pancreatic Islets	Pancreatic Islet
44	chr12:48744000-48745800	Active TSS	Pancreas	Pancrea
45	chr12:48744000-48746000	Active TSS	Fetal Kidney	kidney
46	chr12:48744200-48745200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr12:48744200-48745200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr12:48744200-48745200	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
49	chr12:48744200-48745200	Active TSS	Spleen	Spleen
50	chr12:48744200-48745400	Active TSS	ES-WA7 Cell Line	embryonic stem cell

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