Variant report

Variant	rs7041731
Chromosome Location	chr9:86432595-86432596
allele	A/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	chr9:86432133-86432657	K562	blood:	n/a	n/a
2	POLR2A	chr9:86432395-86433218	SK-N-MC	brain:	n/a	n/a
3	CCNT2	chr9:86432252-86432698	K562	blood:	n/a	chr9:86432668-86432677
4	POLR2A	chr9:86432089-86432745	GM12878	blood:	n/a	n/a
5	POLR2A	chr9:86432189-86432741	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr9:86432560-86432789	H1-neurons	neurons:	n/a	n/a
7	POLR2A	chr9:86432121-86433131	A549	lung:	n/a	n/a
8	POLR2A	chr9:86432420-86432722	HCT-116	colon:	n/a	n/a
9	POLR2A	chr9:86432057-86432750	GM12878	blood:	n/a	n/a
10	EGR1	chr9:86432589-86432805	GM12878	blood:	n/a	chr9:86432760-86432774 chr9:86432696-86432706
11	POLR2A	chr9:86432249-86433148	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr9:86432467-86432721	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr9:86432485-86432742	ECC-1	luminal epithelium:	n/a	n/a
14	HA-E2F1	chr9:86431867-86433290	MCF-7	breast:	n/a	chr9:86432114-86432124 chr9:86432222-86432231 chr9:86432475-86432484 chr9:86432476-86432486
15	RCOR1	chr9:86432289-86432825	K562	blood:	n/a	n/a
16	POLR2A	chr9:86432103-86433547	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr9:86432200-86432821	ProgFib	skin:	n/a	n/a
18	MAX	chr9:86432538-86432757	K562	blood:	n/a	n/a
19	POLR2A	chr9:86432144-86432709	GM12878	blood:	n/a	n/a
20	POLR2A	chr9:86432138-86433041	A549	lung:	n/a	n/a
21	POLR2A	chr9:86432384-86432776	PFSK-1	brain:	n/a	n/a
22	HEY1	chr9:86432168-86433255	HepG2	liver:	n/a	chr9:86432474-86432489 chr9:86432783-86432798 chr9:86432672-86432687 chr9:86432829-86432844 chr9:86432790-86432805
23	EGR1	chr9:86432569-86432957	K562	blood:	n/a	chr9:86432760-86432774 chr9:86432696-86432706
24	TCF3	chr9:86432044-86432728	GM12878	blood:	n/a	chr9:86432141-86432151
25	POLR2A	chr9:86432096-86433143	A549	lung:	n/a	n/a
26	UBTF	chr9:86432045-86433000	K562	blood:	n/a	n/a
27	POLR2A	chr9:86432108-86433024	MCF-7	breast:	n/a	n/a
28	POLR2A	chr9:86432235-86432768	Gliobla	brain:	n/a	n/a
29	POLR2A	chr9:86432149-86432809	ECC-1	luminal epithelium:	n/a	n/a
30	POLR2A	chr9:86432348-86433000	MCF-7	breast:	n/a	n/a
31	ZBTB7A	chr9:86432573-86432736	K562	blood:	n/a	chr9:86432574-86432585
32	POLR2A	chr9:86432151-86432741	A549	lung:	n/a	n/a
33	HEY1	chr9:86432454-86432719	HepG2	liver:	n/a	chr9:86432474-86432489 chr9:86432672-86432687
34	TAF1	chr9:86432060-86432751	HepG2	liver:	n/a	n/a
35	RUNX3	chr9:86432189-86432745	GM12878	blood:	n/a	n/a
36	TCF12	chr9:86432426-86432732	GM12878	blood:	n/a	n/a
37	POLR2A	chr9:86432494-86432718	H1-hESC	embryonic stem cell:	n/a	n/a
38	CHD1	chr9:86431789-86432598	IMR90	lung:	n/a	chr9:86432468-86432478 chr9:86431865-86431875
39	EBF1	chr9:86432091-86432696	GM12878	blood:	n/a	n/a
40	BHLHE40	chr9:86432260-86432688	K562	blood:	n/a	chr9:86432477-86432493
41	POLR2A	chr9:86432551-86432997	HCT-116	colon:	n/a	n/a
42	MAZ	chr9:86432151-86433089	K562	blood:	n/a	chr9:86432333-86432343 chr9:86432473-86432483
43	MXI1	chr9:86432253-86432830	HepG2	liver:	n/a	n/a
44	PAX5	chr9:86432585-86433206	GM12878	blood:	n/a	n/a
45	POLR2A	chr9:86432248-86433328	HepG2	liver:	n/a	n/a
46	ZNF263	chr9:86431582-86433134	HEK293-T-REx	kidney:	n/a	chr9:86431870-86431879 chr9:86432456-86432477 chr9:86431867-86431876 chr9:86432467-86432476
47	POLR2A	chr9:86432492-86432755	K562	blood:	n/a	n/a
48	HA-E2F1	chr9:86432095-86433077	Hela-S3	cervix:	n/a	chr9:86432114-86432124 chr9:86432222-86432231 chr9:86432475-86432484 chr9:86432476-86432486
49	POLR2A	chr9:86432217-86432681	Hela-S3	cervix:	n/a	n/a
50	UBTF	chr9:86432159-86432739	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:86430622..86432919-chr9:86535075..86537489,2	MCF-7	breast:
2	chr9:86321555..86324208-chr9:86431445..86433817,2	MCF-7	breast:
3	chr9:86321469..86324662-chr9:86431245..86433854,3	MCF-7	breast:

Variant related genes	Relation type
GKAP1	TF binding region
ENSG00000165115	Chromatin interaction
ENSG00000135018	Chromatin interaction
ENSG00000254473	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11792634	0.82[AMR][1000 genomes]
rs295270	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs295279	0.83[AMR][1000 genomes]
rs295291	0.83[AMR][1000 genomes]
rs4297107	0.83[AMR][1000 genomes]
rs7851636	0.83[AMR][1000 genomes]
rs9314723	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893513	chr9:86298632-86433459	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv469859	chr9:86398152-86587957	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv482641	chr9:86398152-86587957	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	esv2761538	chr9:86401015-86451943	Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	esv2758192	chr9:86414024-86603602	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
6	esv2759701	chr9:86414024-86603602	Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
7	nsv982312	chr9:86424154-86490046	Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	esv3331113	chr9:86431782-86433830	Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86431000-86433000	Active TSS	A549	lung
2	chr9:86431000-86433200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr9:86431000-86433200	Active TSS	Aorta	Aorta
4	chr9:86431000-86433200	Active TSS	GM12878-XiMat	blood
5	chr9:86431000-86433200	Active TSS	Hela-S3	cervix
6	chr9:86431200-86433000	Active TSS	NHDF-Ad	bronchial
7	chr9:86431200-86433200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr9:86431200-86433400	Active TSS	Thymus	Thymus
9	chr9:86431400-86433000	Active TSS	NHLF	lung
10	chr9:86431400-86433200	Active TSS	Fetal Muscle Leg	muscle
11	chr9:86431400-86433200	Active TSS	HepG2	liver
12	chr9:86431400-86433400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr9:86431400-86433400	Active TSS	Cortex derived primary cultured neurospheres	brain
14	chr9:86431400-86433400	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr9:86431600-86432800	Active TSS	Muscle Satellite Cultured Cells	--
16	chr9:86431600-86433000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr9:86431600-86433000	Active TSS	Primary T cells fromperipheralblood	blood
18	chr9:86431600-86433000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
19	chr9:86431600-86433000	Active TSS	Primary T killer memory cells from peripheral blood	blood
20	chr9:86431600-86433000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr9:86431600-86433000	Active TSS	Brain Inferior Temporal Lobe	brain
22	chr9:86431600-86433000	Active TSS	Fetal Muscle Trunk	muscle
23	chr9:86431600-86433000	Active TSS	Fetal Thymus	thymus
24	chr9:86431600-86433000	Active TSS	NH-A	brain
25	chr9:86431600-86433000	Active TSS	NHEK	skin
26	chr9:86431600-86433000	Active TSS	Osteobl	bone
27	chr9:86431600-86433200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr9:86431600-86433200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr9:86431600-86433200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr9:86431600-86433200	Active TSS	Brain Anterior Caudate	brain
31	chr9:86431600-86433200	Active TSS	Duodenum Smooth Muscle	Duodenum
32	chr9:86431600-86433200	Active TSS	Fetal Intestine Large	intestine
33	chr9:86431600-86433200	Active TSS	Fetal Stomach	stomach
34	chr9:86431600-86433200	Active TSS	Ovary	ovary
35	chr9:86431600-86433200	Active TSS	Psoas Muscle	Psoas
36	chr9:86431600-86433200	Active TSS	Rectal Smooth Muscle	rectum
37	chr9:86431600-86433200	Active TSS	Right Atrium	heart
38	chr9:86431600-86433200	Active TSS	Right Ventricle	heart
39	chr9:86431600-86433200	Active TSS	K562	blood
40	chr9:86431600-86433400	Active TSS	H1 Cell Line	embryonic stem cell
41	chr9:86431600-86433400	Active TSS	HUES48 Cell Line	embryonic stem cell
42	chr9:86431600-86433400	Active TSS	Breast Myoepithelial Primary Cells	Breast
43	chr9:86431600-86433400	Active TSS	Colonic Mucosa	Colon
44	chr9:86431600-86433400	Active TSS	Rectal Mucosa Donor 29	rectum
45	chr9:86431600-86433400	Active TSS	HSMMtube	muscle
46	chr9:86431600-86433800	Active TSS	Stomach Smooth Muscle	stomach
47	chr9:86431800-86432800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr9:86431800-86433000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr9:86431800-86433000	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
50	chr9:86431800-86433000	Active TSS	Primary T killer naive cells fromperipheralblood	blood

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