Variant report

Variant	rs72844341
Chromosome Location	chr11:3829224-3829225
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	POLR2A	chr11:3829170-3830159	HepG2	liver:	n/a	n/a
2	CTCF	chr11:3829137-3829365	MCF-7	breast:	n/a	chr11:3829233-3829251
3	CTCF	chr11:3829180-3829330	HFF	foreskin:	n/a	chr11:3829233-3829251
4	CTCF	chr11:3829027-3829460	GM12878	blood:	n/a	chr11:3829233-3829251
5	CTCF	chr11:3829105-3829359	Medullo	brain:	n/a	chr11:3829233-3829251
6	RFX5	chr11:3829160-3829385	GM12878	blood:	n/a	n/a
7	SMC3	chr11:3829076-3829455	HepG2	liver:	n/a	chr11:3829196-3829203
8	MXI1	chr11:3829202-3829452	K562	blood:	n/a	n/a
9	CTCF	chr11:3829200-3829350	HCM	heart:	n/a	chr11:3829233-3829251
10	CHD2	chr11:3829160-3830082	Hela-S3	cervix:	n/a	n/a
11	ZBTB7A	chr11:3828991-3829923	K562	blood:	n/a	n/a
12	CTCF	chr11:3829160-3829310	K562	blood:	n/a	chr11:3829233-3829251
13	CTCF	chr11:3829160-3829310	HA-sp	spinal cord:	n/a	chr11:3829233-3829251
14	CTCF	chr11:3829180-3829330	GM12870	blood:	n/a	chr11:3829233-3829251
15	CTCF	chr11:3829180-3829330	GM12869	blood:	n/a	chr11:3829233-3829251
16	CTCF	chr11:3829116-3829380	MCF-7	breast:	n/a	chr11:3829233-3829251
17	CTCF	chr11:3829106-3829416	GM19239	blood:	n/a	chr11:3829233-3829251
18	MAX	chr11:3829084-3829266	HepG2	liver:	n/a	n/a
19	CTCF	chr11:3829180-3829330	MCF-7	breast:	n/a	chr11:3829233-3829251
20	CTCF	chr11:3829160-3829310	GM12874	blood:	n/a	chr11:3829233-3829251
21	CTCF	chr11:3829160-3829310	HFF-Myc	foreskin:	n/a	chr11:3829233-3829251
22	BHLHE40	chr11:3829202-3829575	GM12878	blood:	n/a	n/a
23	CTCF	chr11:3829200-3829350	RPTEC	kidney:	n/a	chr11:3829233-3829251
24	CTCF	chr11:3829180-3829330	AG09309	skin:	n/a	chr11:3829233-3829251
25	MAZ	chr11:3829070-3829354	GM12878	blood:	n/a	n/a
26	CTCF	chr11:3829098-3829524	GM19240	blood:	n/a	chr11:3829233-3829251
27	RAD21	chr11:3829046-3829513	H1-hESC	embryonic stem cell:	n/a	chr11:3829231-3829250
28	CTCF	chr11:3829120-3829323	A549	lung:	n/a	chr11:3829233-3829251
29	RAD21	chr11:3829012-3829559	A549	lung:	n/a	chr11:3829231-3829250
30	CHD2	chr11:3829101-3829660	H1-hESC	embryonic stem cell:	n/a	n/a
31	WRNIP1	chr11:3829093-3829596	GM12878	blood:	n/a	n/a
32	RAD21	chr11:3828888-3829914	HCT-116	colon:	n/a	chr11:3829231-3829250
33	CTCF	chr11:3829113-3829387	Hela-S3	cervix:	n/a	chr11:3829233-3829251
34	ZMIZ1	chr11:3829126-3829371	K562	blood:	n/a	n/a
35	SP1	chr11:3829143-3829886	H1-hESC	embryonic stem cell:	n/a	chr11:3829368-3829380 chr11:3829370-3829379 chr11:3829369-3829378 chr11:3829368-3829380 chr11:3829369-3829379 chr11:3829365-3829379
36	POLR2A	chr11:3829158-3829389	Hela-S3	cervix:	n/a	n/a
37	CTCF	chr11:3829160-3829310	GM12869	blood:	n/a	chr11:3829233-3829251
38	RAD21	chr11:3828968-3829432	IMR90	lung:	n/a	chr11:3829231-3829250
39	CTCF	chr11:3829160-3829310	HRE	kidney:	n/a	chr11:3829233-3829251
40	MYC	chr11:3829069-3830076	K562	blood:	n/a	n/a
41	MAFK	chr11:3829003-3829391	K562	blood:	n/a	n/a
42	CTCF	chr11:3829220-3829370	WI-38	lung:	n/a	chr11:3829233-3829251
43	CHD2	chr11:3829049-3829601	K562	blood:	n/a	n/a
44	CTCF	chr11:3829200-3829350	HRPEpiC	eye:	n/a	chr11:3829233-3829251
45	MXI1	chr11:3828840-3831055	SK-N-SH	brain:	n/a	n/a
46	RAD21	chr11:3829082-3829408	GM12878	blood:	n/a	chr11:3829231-3829250
47	POLR2A	chr11:3829116-3830148	Hela-S3	cervix:	n/a	n/a
48	CTCF	chr11:3829180-3829330	HCFaa	heart:	n/a	chr11:3829233-3829251
49	JUND	chr11:3829094-3829656	H1-hESC	embryonic stem cell:	n/a	n/a
50	CTCF	chr11:3829160-3829310	GM12868	blood:	n/a	chr11:3829233-3829251

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr11:3829219-3829269	GM12892	blood:	n/a
2	chr11:3829219-3829269	ovcar-3	ovarian:	n/a
3	chr11:3829219-3829269	Caco-2	colon:	n/a
4	chr11:3829219-3829269	HCT-116	colon:	n/a
5	chr11:3829219-3829269	BJ	skin:	n/a
6	chr11:3829219-3829269	LNCaP	prostate:	n/a
7	chr11:3829219-3829269	ECC-1	luminal epithelium:	n/a
8	chr11:3829219-3829269	A549	lung:	n/a
9	chr11:3829219-3829269	SKMC	muscle:	n/a
10	chr11:3829219-3829269	SAEC	small airway:	n/a
11	chr11:3829219-3829269	SK-N-MC	brain:	n/a
12	chr11:3829219-3829269	PANC-1	pancreas:	n/a
13	chr11:3829219-3829269	HUVEC	blood vessel:	n/a
14	chr11:3829219-3829269	HAEpiC	amniotic membrane:	n/a
15	chr11:3829219-3829269	MCF10A-Er-Src	breast:	n/a
16	chr11:3829219-3829269	SK-N-SH_RA	brain:	n/a
17	chr11:3829219-3829269	SK-N-SH	brain:	n/a
18	chr11:3829219-3829269	T-47D	breast:	n/a
19	chr11:3829219-3829269	BE2_C	brain:	n/a
20	chr11:3829219-3829269	GM06990	blood:	n/a
21	chr11:3829219-3829269	HIPEpiC	eye:	n/a
22	chr11:3829219-3829269	HNPCEpiC	eye:	n/a
23	chr11:3829219-3829269	NHDF-neo	bronchial:	n/a
24	chr11:3829219-3829269	HL-60	blood:	n/a
25	chr11:3829219-3829269	AG09309	skin:	n/a
26	chr11:3829219-3829269	HEEpiC	esophagus:	n/a
27	chr11:3829219-3829269	HMEC	breast:	n/a
28	chr11:3829219-3829269	GM12891	blood:	n/a
29	chr11:3829219-3829269	PFSK-1	brain:	n/a
30	chr11:3829219-3829269	HepG2	liver:	n/a
31	chr11:3829219-3829269	PrEC	prostate:	n/a
32	chr11:3829219-3829269	MCF-7	breast:	n/a
33	chr11:3829219-3829269	GM19239	blood:	n/a
34	chr11:3829219-3829269	HPAEpiC	pulmonary alveolar:	n/a
35	chr11:3829219-3829269	HRE	kidney:	n/a
36	chr11:3829219-3829269	AG09319	gingival:	n/a
37	chr11:3829219-3829269	H1-hESC	embryonic stem cell:	embryo
38	chr11:3829219-3829269	Hepatocyte	liver:	n/a
39	chr11:3829219-3829269	K562	blood:	n/a
40	chr11:3829219-3829269	HRCEpiC	kidney:	n/a
41	chr11:3829219-3829269	Hela-S3	cervix:	n/a
42	chr11:3829219-3829269	NHBE	bronchial:	n/a
43	chr11:3829219-3829269	HCM	heart:	n/a
44	chr11:3829219-3829269	Jurkat	blood:	n/a
45	chr11:3829219-3829269	AoSMC	blood vessel:	n/a
46	chr11:3829219-3829269	NH-A	brain:	n/a
47	chr11:3829219-3829269	HCPEpiC	choroid plexus:	n/a
48	chr11:3829219-3829269	NB4	blood:	n/a
49	chr11:3829219-3829269	ProgFib	skin:	n/a
50	chr11:3829219-3829269	RPTEC	kidney:	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:3828900..3835031-chr11:3840756..3847684,8	K562	blood:
2	chr11:3829046..3832201-chr11:3860687..3864518,3	MCF-7	breast:
3	chr11:3818014..3819859-chr11:3826407..3829369,2	MCF-7	breast:
4	chr11:3827764..3831807-chr11:3860648..3864124,7	K562	blood:
5	chr11:3816139..3821205-chr11:3826361..3831544,11	MCF-7	breast:
6	chr11:3816760..3821195-chr11:3827310..3829330,5	K562	blood:

Variant related genes	Relation type
PGAP2	TF binding region
PGAP2	CpG island
ENSG00000148985	Chromatin interaction
ENSG00000110713	Chromatin interaction
ENSG00000177105	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1049388	1.00[ASN][1000 genomes]
rs11029983	1.00[ASN][1000 genomes]
rs11030043	1.00[ASN][1000 genomes]
rs11030044	1.00[ASN][1000 genomes]
rs11030055	1.00[ASN][1000 genomes]
rs11030173	1.00[ASN][1000 genomes]
rs11600857	1.00[ASN][1000 genomes]
rs11606318	1.00[ASN][1000 genomes]
rs11606483	1.00[ASN][1000 genomes]
rs17173882	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17191448	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17276405	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17276453	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910577	1.00[ASN][1000 genomes]
rs4910846	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910852	1.00[ASN][1000 genomes]
rs4910856	1.00[ASN][1000 genomes]
rs4910857	1.00[ASN][1000 genomes]
rs61896929	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61896930	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61896931	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61896953	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61896954	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61896956	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61896957	1.00[ASN][1000 genomes]
rs61896958	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61896959	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61899361	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61899362	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61899363	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61899392	1.00[ASN][1000 genomes]
rs61899393	1.00[ASN][1000 genomes]
rs6578414	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7101788	1.00[ASN][1000 genomes]
rs72844340	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73430467	1.00[ASN][1000 genomes]
rs74050940	1.00[ASN][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	nsv1049560	chr11:3678259-3980746	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv540907	chr11:3678259-3980746	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1052744	chr11:3739162-4017601	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv1047025	chr11:3750969-4017601	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	esv1803195	chr11:3806490-3924156	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv1046065	chr11:3808818-4049150	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv540909	chr11:3808818-4049150	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	nsv1038220	chr11:3818041-3860024	Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
9	nsv1044882	chr11:3828986-3860024	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:3828800-3829400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr11:3828800-3830200	Active TSS	Fetal Kidney	kidney
3	chr11:3828800-3830600	Flanking Active TSS	Dnd41	blood
4	chr11:3829000-3829400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr11:3829000-3829400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
6	chr11:3829000-3829400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
7	chr11:3829000-3829400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr11:3829000-3829400	Flanking Active TSS	Duodenum Mucosa	Duodenum
9	chr11:3829000-3829400	Enhancers	Fetal Heart	heart
10	chr11:3829000-3829400	Enhancers	Spleen	Spleen
11	chr11:3829000-3829600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr11:3829000-3829600	Flanking Active TSS	Primary B cells from peripheral blood	blood
13	chr11:3829000-3829600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
14	chr11:3829000-3829600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
15	chr11:3829000-3829600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
16	chr11:3829000-3829600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
17	chr11:3829000-3829600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
18	chr11:3829000-3829600	Flanking Active TSS	Colonic Mucosa	Colon
19	chr11:3829000-3829600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
20	chr11:3829000-3829600	Flanking Active TSS	Fetal Muscle Leg	muscle
21	chr11:3829000-3829600	Flanking Active TSS	Fetal Thymus	thymus
22	chr11:3829000-3829600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
23	chr11:3829000-3829600	Flanking Active TSS	HUVEC	blood vessel
24	chr11:3829000-3829800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr11:3829000-3830000	Active TSS	Brain Hippocampus Middle	brain
26	chr11:3829000-3830000	Active TSS	Colon Smooth Muscle	Colon
27	chr11:3829000-3830000	Active TSS	Rectal Smooth Muscle	rectum
28	chr11:3829000-3830000	Active TSS	Right Ventricle	heart
29	chr11:3829000-3830200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr11:3829000-3830200	Active TSS	iPS-15b Cell Line	embryonic stem cell
31	chr11:3829000-3830200	Active TSS	iPS-18 Cell Line	embryonic stem cell
32	chr11:3829000-3830200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr11:3829000-3830200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
34	chr11:3829000-3830200	Flanking Active TSS	Adipose Nuclei	Adipose
35	chr11:3829000-3830200	Active TSS	Brain Anterior Caudate	brain
36	chr11:3829000-3830200	Active TSS	Brain Cingulate Gyrus	brain
37	chr11:3829000-3830200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr11:3829000-3830200	Active TSS	Brain Substantia Nigra	brain
39	chr11:3829000-3830200	Active TSS	A549	lung
40	chr11:3829000-3830400	Active TSS	H1 Cell Line	embryonic stem cell
41	chr11:3829000-3830400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
42	chr11:3829000-3830400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr11:3829000-3830400	Active TSS	Fetal Lung	lung
44	chr11:3829000-3830400	Flanking Active TSS	Stomach Smooth Muscle	stomach
45	chr11:3829000-3830600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
46	chr11:3829000-3830600	Flanking Active TSS	Primary B cells from cord blood	blood
47	chr11:3829000-3830600	Flanking Active TSS	Primary hematopoietic stem cells	blood
48	chr11:3829000-3830600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
49	chr11:3829000-3830600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr11:3829000-3830800	Active TSS	HUES48 Cell Line	embryonic stem cell

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