Variant report

Variant	rs12421579
Chromosome Location	chr11:71291490-71291491
allele	G/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	CTCF	chr11:71290782-71292087	SK-N-SH	brain:	n/a	chr11:71291299-71291320 chr11:71291300-71291313 chr11:71291846-71291867 chr11:71291851-71291869 chr11:71291298-71291314 chr11:71291853-71291866 chr11:71291302-71291310 chr11:71291297-71291315
2	CTCF	chr11:71291013-71292034	HCT-116	colon:	n/a	chr11:71291299-71291320 chr11:71291300-71291313 chr11:71291846-71291867 chr11:71291851-71291869 chr11:71291298-71291314 chr11:71291853-71291866 chr11:71291302-71291310 chr11:71291297-71291315
3	MAX	chr11:71291158-71291625	ECC-1	luminal epithelium:	n/a	n/a
4	RAD21	chr11:71291159-71291555	ECC-1	luminal epithelium:	n/a	chr11:71291298-71291317 chr11:71291300-71291307
5	CTCF	chr11:71291100-71291515	IMR90	lung:	n/a	chr11:71291299-71291320 chr11:71291300-71291313 chr11:71291298-71291314 chr11:71291302-71291310 chr11:71291297-71291315
6	MAX	chr11:71291176-71291557	H1-hESC	embryonic stem cell:	n/a	n/a
7	MAX	chr11:71291158-71291685	A549	lung:	n/a	n/a
8	CTCF	chr11:71291087-71291516	GM12878	blood:	n/a	chr11:71291299-71291320 chr11:71291300-71291313 chr11:71291298-71291314 chr11:71291302-71291310 chr11:71291297-71291315
9	HDAC2	chr11:71291080-71291516	MCF-7	breast:	n/a	chr11:71291420-71291434
10	MAX	chr11:71291165-71291517	K562	blood:	n/a	n/a
11	CTCF	chr11:71291147-71291498	K562	blood:	n/a	chr11:71291299-71291320 chr11:71291300-71291313 chr11:71291298-71291314 chr11:71291302-71291310 chr11:71291297-71291315
12	CTCF	chr11:71291046-71291528	K562	blood:	n/a	chr11:71291299-71291320 chr11:71291300-71291313 chr11:71291298-71291314 chr11:71291302-71291310 chr11:71291297-71291315
13	CTCF	chr11:71291104-71291517	H1-hESC	embryonic stem cell:	n/a	chr11:71291299-71291320 chr11:71291300-71291313 chr11:71291298-71291314 chr11:71291302-71291310 chr11:71291297-71291315
14	MAX	chr11:71291137-71291680	HepG2	liver:	n/a	n/a
15	MAX	chr11:71291180-71291661	MCF-7	breast:	n/a	n/a
16	E2F6	chr11:71291151-71291578	H1-hESC	embryonic stem cell:	n/a	n/a
17	CBX3	chr11:71291200-71291647	HCT-116	colon:	n/a	n/a
18	E2F6	chr11:71291165-71291709	H1-hESC	embryonic stem cell:	n/a	n/a
19	MAX	chr11:71291172-71291547	A549	lung:	n/a	n/a
20	MAX	chr11:71291205-71291542	H1-hESC	embryonic stem cell:	n/a	n/a
21	FOXM1	chr11:71291081-71291519	GM12878	blood:	n/a	n/a
22	MAX	chr11:71291039-71291753	HCT-116	colon:	n/a	n/a
23	CTCF	chr11:71291110-71291930	HepG2	liver:	n/a	chr11:71291299-71291320 chr11:71291300-71291313 chr11:71291846-71291867 chr11:71291851-71291869 chr11:71291298-71291314 chr11:71291853-71291866 chr11:71291302-71291310 chr11:71291297-71291315
24	CTCF	chr11:71291094-71291527	K562	blood:	n/a	chr11:71291299-71291320 chr11:71291300-71291313 chr11:71291298-71291314 chr11:71291302-71291310 chr11:71291297-71291315
25	RAD21	chr11:71291205-71291512	MCF-7	breast:	n/a	chr11:71291298-71291317 chr11:71291300-71291307
26	CTCF	chr11:71291066-71291497	H1-hESC	embryonic stem cell:	n/a	chr11:71291299-71291320 chr11:71291300-71291313 chr11:71291298-71291314 chr11:71291302-71291310 chr11:71291297-71291315
27	CTCF	chr11:71291183-71291561	MCF-7	breast:	n/a	chr11:71291299-71291320 chr11:71291300-71291313 chr11:71291298-71291314 chr11:71291302-71291310 chr11:71291297-71291315
28	E2F6	chr11:71291271-71291498	K562	blood:	n/a	n/a
29	E2F6	chr11:71291169-71291612	A549	lung:	n/a	n/a
30	MAX	chr11:71291183-71291517	Hela-S3	cervix:	n/a	n/a
31	CTCF	chr11:71291017-71291649	HCT-116	colon:	n/a	chr11:71291299-71291320 chr11:71291300-71291313 chr11:71291298-71291314 chr11:71291302-71291310 chr11:71291297-71291315
32	MAX	chr11:71291218-71291527	K562	blood:	n/a	n/a
33	CTCF	chr11:71291340-71291490	HAc	cerebellar:	n/a	n/a
34	MAX	chr11:71291178-71291578	H1-hESC	embryonic stem cell:	n/a	n/a
35	CTCF	chr11:71291340-71291490	HFF-Myc	foreskin:	n/a	n/a
36	MAX	chr11:71291173-71291664	ECC-1	luminal epithelium:	n/a	n/a
37	CTCF	chr11:71291013-71291904	MCF-7	breast:	n/a	chr11:71291299-71291320 chr11:71291300-71291313 chr11:71291846-71291867 chr11:71291851-71291869 chr11:71291298-71291314 chr11:71291853-71291866 chr11:71291302-71291310 chr11:71291297-71291315
38	MAX	chr11:71291075-71291679	HCT-116	colon:	n/a	n/a
39	MAX	chr11:71291167-71291610	HepG2	liver:	n/a	n/a
40	MAX	chr11:71291119-71291757	MCF-7	breast:	n/a	n/a
41	BACH1	chr11:71291175-71291514	H1-hESC	embryonic stem cell:	n/a	n/a
42	CTCF	chr11:71290732-71292117	A549	lung:	n/a	chr11:71291299-71291320 chr11:71291300-71291313 chr11:71291846-71291867 chr11:71291851-71291869 chr11:71291298-71291314 chr11:71291853-71291866 chr11:71291302-71291310 chr11:71291297-71291315

No.	Distal block	Cell Line	Cell type
1	chr11:71163473..71165824-chr11:71289975..71292795,2	MCF-7	breast:
2	chr11:71278406..71279386-chr11:71291430..71292089,2	MCF-7	breast:
3	chr11:71278394..71279845-chr11:71290961..71292008,7	MCF-7	breast:
4	chr11:71185954..71187783-chr11:71290414..71293087,2	MCF-7	breast:
5	chr11:71158649..71161220-chr11:71291218..71293129,2	MCF-7	breast:

Variant related genes	Relation type
KRTAP5-14P	TF binding region
ENSG00000254682	Chromatin interaction
ENSG00000172890	Chromatin interaction
ENSG00000248903	Chromatin interaction
ENSG00000172893	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10751118	0.84[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10751119	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10898347	0.90[CHB][hapmap];0.80[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11607338	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2015464	0.89[ASN][1000 genomes]
rs4081429	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap]

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	nsv530623	chr11:71088949-72020418	Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
2	esv3372246	chr11:71223101-71435819	Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv825988	chr11:71277262-71294289	ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv975851	chr11:71278888-71295301	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:71289000-71291600	Weak transcription	Gastric	stomach
2	chr11:71289400-71291600	Enhancers	Fetal Muscle Leg	muscle
3	chr11:71290400-71292000	Enhancers	H1 Cell Line	embryonic stem cell
4	chr11:71290400-71293400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr11:71290400-71293600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr11:71290600-71291600	Enhancers	Skeletal Muscle Male	skeletal muscle
7	chr11:71290600-71291800	Enhancers	Duodenum Smooth Muscle	Duodenum
8	chr11:71290800-71291600	Enhancers	Brain Substantia Nigra	brain
9	chr11:71290800-71291800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr11:71290800-71292000	Enhancers	Adipose Nuclei	Adipose
11	chr11:71290800-71292000	Enhancers	GM12878-XiMat	blood
12	chr11:71291000-71291600	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr11:71291000-71291600	Enhancers	Fetal Kidney	kidney
14	chr11:71291000-71291800	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr11:71291000-71293000	Enhancers	HepG2	liver
16	chr11:71291200-71291600	Enhancers	Stomach Smooth Muscle	stomach
17	chr11:71291200-71291800	Enhancers	Brain Cingulate Gyrus	brain
18	chr11:71291200-71291800	Enhancers	Fetal Intestine Large	intestine
19	chr11:71291200-71292600	Weak transcription	Pancreas	Pancrea
20	chr11:71291200-71293000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr11:71291400-71291600	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr11:71291400-71291600	Flanking Active TSS	A549	lung
23	chr11:71291400-71291600	Flanking Bivalent TSS/Enh	K562	blood
24	chr11:71291400-71291600	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
25	chr11:71291400-71291800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr11:71291400-71291800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr11:71291400-71291800	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr11:71291400-71291800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
29	chr11:71291400-71291800	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
30	chr11:71291400-71291800	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr11:71291400-71291800	Enhancers	Hela-S3	cervix
32	chr11:71291400-71295200	Weak transcription	Right Atrium	heart

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