Variant report

Variant	rs3829260
Chromosome Location	chr11:119598729-119598730
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	CTCF	chr11:119598541-119598777	MCF-7	breast:	n/a	chr11:119598571-119598584
2	CTCF	chr11:119598580-119598730	BE2_C	brain:	n/a	n/a
3	CTCF	chr11:119598580-119598730	K562	blood:	n/a	n/a
4	ZBTB7A	chr11:119598441-119598892	ECC-1	luminal epithelium:	n/a	chr11:119598688-119598696
5	CTCF	chr11:119598720-119598870	HEK293	kidney:	n/a	n/a
6	CTCF	chr11:119598580-119598730	AG09319	gingival:	n/a	n/a
7	CTCF	chr11:119598620-119598770	RPTEC	kidney:	n/a	n/a
8	CTCF	chr11:119598580-119598730	A549	lung:	n/a	n/a
9	CTCF	chr11:119598553-119598736	GM10248	blood:	n/a	chr11:119598571-119598584
10	POLR2A	chr11:119598486-119598939	GM12878	blood:	n/a	n/a
11	CTCF	chr11:119598640-119598790	GM06990	blood:	n/a	n/a
12	CTCF	chr11:119598600-119598750	HFF	foreskin:	n/a	n/a
13	CTCF	chr11:119598580-119598730	GM12865	blood:	n/a	n/a
14	SMC3	chr11:119598712-119599080	GM12878	blood:	n/a	n/a
15	CTCF	chr11:119598588-119598741	MCF-7	breast:	n/a	n/a
16	CTCF	chr11:119598580-119598730	HRPEpiC	eye:	n/a	n/a
17	CTCF	chr11:119598557-119598791	LNCaP	prostate:	n/a	chr11:119598571-119598584
18	CTCF	chr11:119598580-119598730	GM12878	blood:	n/a	n/a
19	BHLHE40	chr11:119598579-119598839	GM12878	blood:	n/a	chr11:119598642-119598658
20	CTCF	chr11:119598513-119598771	IMR90	lung:	n/a	chr11:119598571-119598584
21	MAZ	chr11:119598594-119598748	HepG2	liver:	n/a	n/a
22	CTCF	chr11:119598580-119598730	Caco-2	colon:	n/a	n/a
23	CTCF	chr11:119598620-119598770	HCFaa	heart:	n/a	n/a
24	CTCF	chr11:119598574-119598746	Pancreas_OC	pancreas:	n/a	n/a
25	PAX5	chr11:119598538-119598779	GM12892	blood:	n/a	n/a
26	ZNF143	chr11:119598474-119598858	GM12878	blood:	n/a	n/a
27	POLR2A	chr11:119598115-119600381	H1-neurons	neurons:	n/a	n/a
28	POLR2A	chr11:119598418-119599330	HL-60	blood:	n/a	n/a
29	CTCF	chr11:119598620-119598770	GM12878	blood:	n/a	n/a
30	POLR2A	chr11:119598105-119599239	H1-neurons	neurons:	n/a	n/a
31	CTCF	chr11:119598620-119598770	GM12872	blood:	n/a	n/a
32	RUNX3	chr11:119598461-119598746	GM12878	blood:	n/a	n/a
33	SIN3A	chr11:119597072-119600964	H1-hESC	embryonic stem cell:	n/a	chr11:119598510-119598523 chr11:119597118-119597129 chr11:119599794-119599805 chr11:119599846-119599857 chr11:119599845-119599858
34	CTCF	chr11:119598620-119598770	HRE	kidney:	n/a	n/a
35	CTCF	chr11:119598600-119598750	NHLF	lung:	n/a	n/a
36	CTCF	chr11:119598539-119598816	GM19239	blood:	n/a	chr11:119598571-119598584
37	CHD1	chr11:119598392-119599326	GM12878	blood:	n/a	n/a
38	CTCF	chr11:119598580-119598730	GM12874	blood:	n/a	n/a
39	REST	chr11:119597919-119600693	H1-neurons	neurons:	n/a	chr11:119599848-119599861 chr11:119599304-119599317 chr11:119598617-119598630 chr11:119599848-119599861 chr11:119599845-119599858 chr11:119600480-119600493 chr11:119600483-119600496 chr11:119599290-119599303 chr11:119598510-119598523 chr11:119599302-119599320 chr11:119599040-119599053
40	CTCF	chr11:119598580-119598730	SAEC	small airway:	n/a	n/a
41	CTCF	chr11:119598470-119598900	K562	blood:	n/a	chr11:119598571-119598584
42	CTCF	chr11:119598620-119598770	HA-sp	spinal cord:	n/a	n/a
43	CTCF	chr11:119598580-119598730	AoAF	blood vessel:	n/a	n/a
44	CTCF	chr11:119598567-119598748	Kidney_OC	kidney:	n/a	chr11:119598571-119598584
45	CTCF	chr11:119598600-119598750	NHEK	skin:	n/a	n/a
46	RAD21	chr11:119598508-119598745	SK-N-SH_RA	brain:	n/a	n/a
47	CTCF	chr11:119598660-119598810	Hela-S3	cervix:	n/a	n/a
48	SMC3	chr11:119598624-119598734	Hela-S3	cervix:	n/a	n/a
49	MAZ	chr11:119597671-119601057	IMR90	lung:	n/a	chr11:119598584-119598594 chr11:119598070-119598085 chr11:119598072-119598087 chr11:119598074-119598083 chr11:119598074-119598083 chr11:119598072-119598085 chr11:119598073-119598082 chr11:119598073-119598083 chr11:119598075-119598082 chr11:119598074-119598084 chr11:119598073-119598084 chr11:119598073-119598083 chr11:119598072-119598085 chr11:119598073-119598084 chr11:119598072-119598085
50	CTCF	chr11:119598600-119598750	GM12868	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr11:119598725-119598775	AG09319	gingival:	n/a
2	chr11:119598725-119598775	HCM	heart:	n/a
3	chr11:119598725-119598775	PANC-1	pancreas:	n/a
4	chr11:119598725-119598775	HIPEpiC	eye:	n/a
5	chr11:119598725-119598775	HAEpiC	amniotic membrane:	n/a
6	chr11:119598725-119598775	AoSMC	blood vessel:	n/a
7	chr11:119598725-119598775	BE2_C	brain:	n/a
8	chr11:119598725-119598775	H1-hESC	embryonic stem cell:	embryo
9	chr11:119598725-119598775	HEK293	kidney:	embryo
10	chr11:119598725-119598775	AG04450	lung:	fetal
11	chr11:119598725-119598775	HCF	heart:	n/a
12	chr11:119598725-119598775	HepG2	liver:	n/a
13	chr11:119598725-119598775	LNCaP	prostate:	n/a
14	chr11:119598725-119598775	HRCEpiC	kidney:	n/a
15	chr11:119598725-119598775	GM12891	blood:	n/a
16	chr11:119598725-119598775	SK-N-SH	brain:	n/a
17	chr11:119598725-119598775	RPTEC	kidney:	n/a
18	chr11:119598725-119598775	GM12878	blood:	n/a
19	chr11:119598725-119598775	NH-A	brain:	n/a
20	chr11:119598725-119598775	CMK	blood:	n/a
21	chr11:119598725-119598775	HPAEpiC	pulmonary alveolar:	n/a
22	chr11:119598725-119598775	NHDF-neo	bronchial:	n/a
23	chr11:119598725-119598775	MCF10A-Er-Src	breast:	n/a
24	chr11:119598725-119598775	HL-60	blood:	n/a
25	chr11:119598725-119598775	GM12892	blood:	n/a
26	chr11:119598725-119598775	U87	brain:	n/a
27	chr11:119598725-119598775	PrEC	prostate:	n/a
28	chr11:119598725-119598775	SKMC	muscle:	n/a
29	chr11:119598725-119598775	NHBE	bronchial:	n/a
30	chr11:119598725-119598775	GM06990	blood:	n/a
31	chr11:119598725-119598775	Hepatocyte	liver:	n/a
32	chr11:119598725-119598775	T-47D	breast:	n/a
33	chr11:119598725-119598775	AG04449	skin:	fetal
34	chr11:119598725-119598775	PFSK-1	brain:	n/a
35	chr11:119598725-119598775	SK-N-MC	brain:	n/a
36	chr11:119598725-119598775	NT2-D1	testis:	n/a
37	chr11:119598725-119598775	HUVEC	blood vessel:	n/a
38	chr11:119598725-119598775	ovcar-3	ovarian:	n/a
39	chr11:119598725-119598775	A549	lung:	n/a
40	chr11:119598725-119598775	HEEpiC	esophagus:	n/a
41	chr11:119598725-119598775	AG10803	skin:	n/a
42	chr11:119598725-119598775	SK-N-SH_RA	brain:	n/a
43	chr11:119598725-119598775	MCF-7	breast:	n/a
44	chr11:119598725-119598775	BJ	skin:	n/a
45	chr11:119598725-119598775	K562	blood:	n/a
46	chr11:119598725-119598775	Hela-S3	cervix:	n/a
47	chr11:119598725-119598775	IMR90	lung:	fetal
48	chr11:119598725-119598775	ECC-1	luminal epithelium:	n/a
49	chr11:119598725-119598775	HCPEpiC	choroid plexus:	n/a
50	chr11:119598725-119598775	GM19239	blood:	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:119537222..119537812-chr11:119598187..119599149,2	MCF-7	breast:
2	chr11:119564818..119565650-chr11:119598208..119598847,2	MCF-7	breast:
3	chr11:119593045..119595193-chr11:119597284..119598893,2	K562	blood:
4	chr11:119598280..119601010-chr11:119990751..119994590,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000254854	TF binding region
ENSG00000254854	CpG island
ENSG00000137699	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10790339	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10892444	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10892446	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11217429	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11217430	0.80[EUR][1000 genomes]
rs11217434	0.80[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs11217437	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11217438	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11217440	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11217441	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11607610	0.81[EUR][1000 genomes]
rs12418662	0.81[EUR][1000 genomes]
rs12421434	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12421466	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12793075	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12796806	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12797914	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12800445	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1876795	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2136420	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2136421	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2368936	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35248712	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4245206	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4505073	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4936496	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4938718	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4938719	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4938720	0.80[AFR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7952366	0.81[EUR][1000 genomes]
rs9666263	0.81[EUR][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	nsv898421	chr11:119499014-119631325	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv898422	chr11:119518006-119601779	Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv898423	chr11:119541332-119659753	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv1051769	chr11:119572865-119630769	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv1037739	chr11:119592989-119630641	Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	esv3364090	chr11:119598267-119601315	Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:119596600-119598800	Flanking Active TSS	Brain Hippocampus Middle	brain
2	chr11:119596600-119600400	Active TSS	Esophagus	oesophagus
3	chr11:119597000-119599200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
4	chr11:119597000-119599200	Flanking Active TSS	GM12878-XiMat	blood
5	chr11:119597200-119598800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
6	chr11:119597200-119599200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
7	chr11:119597200-119599200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr11:119597200-119599200	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
9	chr11:119597200-119599600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
10	chr11:119597200-119600400	Active TSS	H1 Cell Line	embryonic stem cell
11	chr11:119597200-119600400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr11:119597200-119600400	Active TSS	iPS-15b Cell Line	embryonic stem cell
13	chr11:119597200-119600800	Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr11:119597200-119601000	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr11:119597200-119601000	Active TSS	H9 Cell Line	embryonic stem cell
16	chr11:119597400-119598800	Flanking Active TSS	Stomach Smooth Muscle	stomach
17	chr11:119597400-119599200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
18	chr11:119597400-119600600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr11:119597400-119600800	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr11:119597400-119601000	Active TSS	HUES64 Cell Line	embryonic stem cell
21	chr11:119597400-119601000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr11:119597600-119598800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
23	chr11:119597600-119598800	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
24	chr11:119597600-119598800	Flanking Active TSS	Right Ventricle	heart
25	chr11:119597600-119598800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
26	chr11:119597600-119599000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr11:119597600-119599000	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
28	chr11:119597600-119599200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr11:119597600-119599400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
30	chr11:119597600-119599400	Flanking Active TSS	Adipose Nuclei	Adipose
31	chr11:119597600-119599400	Flanking Active TSS	Colonic Mucosa	Colon
32	chr11:119597600-119601000	Active TSS	Fetal Kidney	kidney
33	chr11:119597800-119598800	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
34	chr11:119597800-119598800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
35	chr11:119597800-119598800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr11:119597800-119598800	Flanking Active TSS	HUVEC	blood vessel
37	chr11:119597800-119599000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr11:119597800-119599400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr11:119597800-119600400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr11:119597800-119600400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr11:119597800-119600400	Active TSS	HUES6 Cell Line	embryonic stem cell
42	chr11:119597800-119600400	Active TSS	iPS-20b Cell Line	embryonic stem cell
43	chr11:119597800-119600400	Active TSS	HMEC	breast
44	chr11:119597800-119600400	Active TSS	NHEK	skin
45	chr11:119597800-119600800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr11:119597800-119600800	Active TSS	Fetal Brain Female	brain
47	chr11:119597800-119601000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr11:119597800-119601000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr11:119598000-119599000	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
50	chr11:119598000-119599000	Bivalent/Poised TSS	Brain Germinal Matrix	brain

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