Variant report

Variant	rs1925369
Chromosome Location	chr11:34381075-34381076
allele	C/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	chr11:34380713-34381330	Medullo	brain:	n/a	chr11:34380718-34380731 chr11:34381202-34381220 chr11:34381197-34381218
2	CTCF	chr11:34380940-34381090	HPF	lung:	n/a	n/a
3	MAX	chr11:34378502-34381150	Hela-S3	cervix:	n/a	chr11:34379281-34379291 chr11:34380691-34380706
4	RAD21	chr11:34380685-34381272	K562	blood:	n/a	chr11:34381200-34381219
5	CTCF	chr11:34380461-34381341	K562	blood:	n/a	chr11:34380718-34380731 chr11:34381202-34381220 chr11:34380591-34380604 chr11:34381197-34381218
6	CBX3	chr11:34380473-34381189	K562	blood:	n/a	n/a
7	CTCF	chr11:34380960-34381110	GM12864	blood:	n/a	n/a
8	CTCF	chr11:34380880-34381123	HepG2	liver:	n/a	n/a
9	CTCF	chr11:34380727-34381329	HUVEC	blood vessel:	n/a	chr11:34381202-34381220 chr11:34381197-34381218
10	CTCF	chr11:34380342-34381406	GM12878	blood:	n/a	chr11:34380718-34380731 chr11:34381202-34381220 chr11:34380591-34380604 chr11:34381197-34381218
11	CTCF	chr11:34380628-34381307	GM12878	blood:	n/a	chr11:34380718-34380731 chr11:34381202-34381220 chr11:34381197-34381218
12	CEBPB	chr11:34380574-34381232	Hela-S3	cervix:	n/a	chr11:34381153-34381166 chr11:34380965-34380978
13	CTCF	chr11:34380594-34381371	T-47D	breast:	n/a	chr11:34380718-34380731 chr11:34381202-34381220 chr11:34381197-34381218
14	CTCF	chr11:34380960-34381110	GM12871	blood:	n/a	n/a
15	CTCF	chr11:34380531-34381402	A549	lung:	n/a	chr11:34380718-34380731 chr11:34381202-34381220 chr11:34380591-34380604 chr11:34381197-34381218
16	CTCF	chr11:34380524-34381434	A549	lung:	n/a	chr11:34380718-34380731 chr11:34381202-34381220 chr11:34380591-34380604 chr11:34381197-34381218
17	CTCF	chr11:34381000-34381150	BE2_C	brain:	n/a	n/a
18	RAD21	chr11:34380463-34381483	MCF-7	breast:	n/a	chr11:34381200-34381219 chr11:34380673-34380685
19	CTCF	chr11:34380841-34381310	LNCaP	prostate:	n/a	chr11:34381202-34381220 chr11:34381197-34381218
20	CHD2	chr11:34380410-34381164	GM12878	blood:	n/a	n/a
21	JUND	chr11:34380738-34381136	K562	blood:	n/a	n/a
22	MAX	chr11:34380459-34381082	GM12878	blood:	n/a	chr11:34380691-34380706
23	ARID3A	chr11:34380766-34381328	K562	blood:	n/a	n/a
24	MAX	chr11:34380185-34381102	MCF-7	breast:	n/a	chr11:34380691-34380706
25	RFX5	chr11:34380733-34381183	GM12878	blood:	n/a	n/a
26	CTCF	chr11:34380669-34381307	GM13977	blood:	n/a	chr11:34380718-34380731 chr11:34381202-34381220 chr11:34381197-34381218
27	CTCF	chr11:34380892-34381113	MCF-7	breast:	n/a	n/a
28	CTCF	chr11:34380960-34381110	HPF	lung:	n/a	n/a
29	FOXM1	chr11:34380655-34381269	GM12878	blood:	n/a	n/a
30	ZC3H11A	chr11:34380899-34381370	K562	blood:	n/a	n/a
31	MAFK	chr11:34380092-34381291	Hela-S3	cervix:	n/a	n/a
32	JUND	chr11:34380706-34381357	H1-hESC	embryonic stem cell:	n/a	chr11:34381227-34381236
33	FOSL2	chr11:34380811-34381189	A549	lung:	n/a	n/a
34	CTCF	chr11:34380799-34381331	LNCaP	prostate:	n/a	chr11:34381202-34381220 chr11:34381197-34381218
35	SIN3A	chr11:34380780-34381115	GM12878	blood:	n/a	n/a
36	CTCF	chr11:34380894-34381113	GM13976	blood:	n/a	n/a
37	CTCF	chr11:34380647-34381324	Pancreas_OC	pancreas:	n/a	chr11:34380718-34380731 chr11:34381202-34381220 chr11:34381197-34381218
38	RAD21	chr11:34380432-34381413	H1-hESC	embryonic stem cell:	n/a	chr11:34381200-34381219 chr11:34380673-34380685
39	CTCF	chr11:34380940-34381090	HL-60	blood:	n/a	n/a
40	MAZ	chr11:34380567-34381170	GM12878	blood:	n/a	chr11:34380691-34380706
41	MXI1	chr11:34378457-34381133	Hela-S3	cervix:	n/a	n/a
42	CTCF	chr11:34380627-34381373	Spleen_OC	spleen:	n/a	chr11:34380718-34380731 chr11:34381202-34381220 chr11:34381197-34381218
43	TCF12	chr11:34379084-34381370	A549	lung:	n/a	n/a
44	CTCF	chr11:34380602-34381140	Gliobla	brain:	n/a	chr11:34380718-34380731
45	RAD21	chr11:34380469-34381380	SK-N-SH_RA	brain:	n/a	chr11:34381200-34381219 chr11:34380673-34380685
46	SMC3	chr11:34380074-34381362	HepG2	liver:	n/a	n/a
47	FOS	chr11:34380998-34381186	MCF10A-Er-Src	breast:	n/a	n/a
48	CTCF	chr11:34380940-34381090	AG10803	skin:	n/a	n/a
49	NFIC	chr11:34380521-34381145	ECC-1	luminal epithelium:	n/a	n/a
50	MAZ	chr11:34380559-34381172	K562	blood:	n/a	chr11:34380691-34380706

No.	Distal block	Cell Line	Cell type
1	chr11:34171215..34172003-chr11:34380711..34381705,3	MCF-7	breast:
2	chr11:34380939..34381848-chr11:34514131..34515008,2	MCF-7	breast:
3	chr11:34368701..34370901-chr11:34379752..34381357,2	K562	blood:
4	chr11:34195400..34196504-chr11:34379832..34381736,16	MCF-7	breast:
5	chr11:34071981..34076766-chr11:34377622..34383038,7	MCF-7	breast:
6	chr11:34187084..34188044-chr11:34380825..34381630,2	MCF-7	breast:
7	chr11:34126304..34129768-chr11:34376546..34381116,4	MCF-7	breast:
8	chr11:34018304..34019124-chr11:34380429..34381489,5	MCF-7	breast:
9	chr11:34171073..34172022-chr11:34380697..34381569,3	MCF-7	breast:
10	chr11:34183076..34183659-chr11:34380555..34381170,2	K562	blood:
11	chr11:34186780..34187813-chr11:34380499..34381345,5	MCF-7	breast:
12	chr11:34197728..34198296-chr11:34380470..34381106,2	MCF-7	breast:
13	chr11:34380153..34381078-chr20:60718993..60719935,2	Hela-S3	cervix:
14	chr11:34018651..34019172-chr11:34380715..34381485,2	K562	blood:
15	chr11:34194851..34196566-chr11:34380231..34381621,20	MCF-7	breast:
16	chr11:33879110..33879929-chr11:34380779..34381404,2	MCF-7	breast:
17	chr11:34125543..34130810-chr11:34377372..34382966,13	MCF-7	breast:
18	chr11:34170082..34170878-chr11:34380526..34381351,2	K562	blood:
19	chr11:34127120..34127834-chr11:34380752..34381319,3	MCF-7	breast:
20	chr11:34380524..34381238-chr11:34489841..34490388,3	K562	blood:
21	chr11:33879158..33879864-chr11:34380802..34381795,2	MCF-7	breast:
22	chr11:34380514..34381443-chr11:34513937..34515065,4	K562	blood:

Variant related genes	Relation type
ABTB2	TF binding region
ENSG00000135372	Chromatin interaction
ENSG00000135387	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs2611134	0.98[EUR][1000 genomes]
rs61880787	0.81[AFR][1000 genomes]
rs61880808	0.85[AFR][1000 genomes]
rs7927163	0.88[AFR][1000 genomes]
rs7928060	0.89[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897205	chr11:34248229-34507213	Enhancers Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv897207	chr11:34253683-34621004	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv897208	chr11:34257064-34562247	Strong transcription Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv897209	chr11:34309519-34548906	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv897210	chr11:34349427-34381075	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1925369	CAT	Cis_1M	lymphoblastoid	RTeQTL
rs1925369	CAT	cis	parietal	SCAN

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:34376400-34381200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr11:34377600-34381200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
3	chr11:34378000-34381200	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr11:34378000-34381200	Active TSS	A549	lung
5	chr11:34378200-34381200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
6	chr11:34378200-34381200	Active TSS	Colon Smooth Muscle	Colon
7	chr11:34378200-34381200	Active TSS	Fetal Kidney	kidney
8	chr11:34378400-34381200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr11:34378600-34381200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
10	chr11:34378600-34381200	Active TSS	Duodenum Smooth Muscle	Duodenum
11	chr11:34378600-34381200	Active TSS	Stomach Mucosa	stomach
12	chr11:34378800-34381200	Active TSS	Brain Anterior Caudate	brain
13	chr11:34379000-34381200	Active TSS	Thymus	Thymus
14	chr11:34379200-34381200	Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr11:34379200-34381400	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr11:34379800-34381200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
17	chr11:34379800-34381400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
18	chr11:34379800-34381400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr11:34379800-34381400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr11:34380000-34381200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr11:34380000-34381200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr11:34380000-34381200	Flanking Active TSS	Primary B cells from cord blood	blood
23	chr11:34380000-34381200	Flanking Active TSS	Primary B cells from peripheral blood	blood
24	chr11:34380000-34381200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
25	chr11:34380000-34381200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr11:34380000-34381200	Flanking Active TSS	Liver	Liver
27	chr11:34380400-34381200	Active TSS	Primary T helper naive cells from peripheral blood	blood
28	chr11:34380400-34381200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
29	chr11:34380600-34381200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr11:34380600-34381200	Active TSS	Brain Substantia Nigra	brain
31	chr11:34380600-34381200	Active TSS	HSMMtube	muscle
32	chr11:34380600-34381200	Active TSS	NHDF-Ad	bronchial
33	chr11:34380600-34381400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
34	chr11:34380800-34381200	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr11:34380800-34381200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
36	chr11:34380800-34381200	Active TSS	Primary T cells from cord blood	blood
37	chr11:34380800-34381200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
38	chr11:34380800-34381200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr11:34380800-34381200	Active TSS	Muscle Satellite Cultured Cells	--
40	chr11:34380800-34381200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr11:34380800-34381200	Active TSS	Adipose Nuclei	Adipose
42	chr11:34380800-34381200	Active TSS	Brain Cingulate Gyrus	brain
43	chr11:34380800-34381200	Active TSS	Brain Hippocampus Middle	brain
44	chr11:34380800-34381200	Active TSS	Brain Inferior Temporal Lobe	brain
45	chr11:34380800-34381200	Active TSS	Duodenum Mucosa	Duodenum
46	chr11:34380800-34381200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
47	chr11:34380800-34381200	Active TSS	Fetal Lung	lung
48	chr11:34380800-34381200	Active TSS	Fetal Muscle Leg	muscle
49	chr11:34380800-34381200	Active TSS	Fetal Stomach	stomach
50	chr11:34380800-34381200	Active TSS	Rectal Mucosa Donor 29	rectum

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