Variant report

Variant	rs7025554
Chromosome Location	chr9:95898531-95898532
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	FOXA1	chr9:95898419-95898725	HepG2	liver:	n/a	chr9:95898587-95898602
2	CEBPB	chr9:95898488-95898598	HepG2	liver:	n/a	n/a
3	POLR2A	chr9:95898402-95898655	HepG2	liver:	n/a	n/a
4	FOXA2	chr9:95898391-95898691	HepG2	liver:	n/a	n/a
5	POLR2A	chr9:95898490-95898540	ProgFib	skin:	n/a	n/a
6	ZNF384	chr9:95898492-95898785	K562	blood:	n/a	n/a
7	FOXA1	chr9:95898362-95898685	T-47D	breast:	n/a	chr9:95898587-95898602
8	FOXA1	chr9:95898421-95898710	T-47D	breast:	n/a	chr9:95898587-95898602
9	SP1	chr9:95898385-95898720	A549	lung:	n/a	n/a
10	FOXA1	chr9:95898308-95898708	HepG2	liver:	n/a	chr9:95898587-95898602
11	FOXA2	chr9:95898278-95898743	A549	lung:	n/a	n/a
12	MYC	chr9:95898490-95898574	HepG2	liver:	n/a	n/a
13	TBP	chr9:95898507-95898661	HepG2	liver:	n/a	n/a
14	FOXA1	chr9:95898499-95898681	ECC-1	luminal epithelium:	n/a	chr9:95898587-95898602
15	FOXA1	chr9:95898334-95898703	HepG2	liver:	n/a	chr9:95898587-95898602
16	FOXA2	chr9:95898409-95898900	A549	lung:	n/a	n/a
17	FOXA1	chr9:95898354-95898704	HepG2	liver:	n/a	chr9:95898587-95898602
18	FOXP2	chr9:95898359-95898657	PFSK-1	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:95895042..95899051-chr9:95945154..95949540,5	MCF-7	breast:
2	chr9:95893768..95895658-chr9:95897377..95900133,3	K562	blood:
3	chr9:95856253..95862485-chr9:95892353..95899486,12	MCF-7	breast:
4	chr9:95897165..95898764-chr9:95898859..95901008,2	K562	blood:
5	chr9:95855662..95862507-chr9:95894736..95899302,16	MCF-7	breast:

Variant related genes	Relation type
NINJ1	TF binding region
ENSG00000223446	Chromatin interaction
ENSG00000165238	Chromatin interaction
ENSG00000165233	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11792871	0.89[AFR][1000 genomes]
rs12337469	1.00[CEU][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12342200	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73524733	0.95[EUR][1000 genomes]
rs7867389	0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7867526	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526296	chr9:95708192-96030392	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv1035230	chr9:95770249-95934982	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv893576	chr9:95789960-96158277	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	esv1824329	chr9:95811604-95921347	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv893579	chr9:95855100-95923091	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv893580	chr9:95855100-96099377	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	nsv893581	chr9:95872216-95930334	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95896000-95899200	Enhancers	Fetal Brain Male	brain
2	chr9:95897200-95898600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr9:95897200-95898600	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr9:95897200-95898600	Enhancers	Muscle Satellite Cultured Cells	--
5	chr9:95897200-95898600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr9:95897200-95898600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr9:95897200-95898600	Enhancers	Brain Angular Gyrus	brain
8	chr9:95897200-95898600	Enhancers	Brain Substantia Nigra	brain
9	chr9:95897200-95898600	Enhancers	Fetal Brain Female	brain
10	chr9:95897200-95898600	Enhancers	Ovary	ovary
11	chr9:95897200-95898600	Enhancers	Right Ventricle	heart
12	chr9:95897200-95898600	Enhancers	A549	lung
13	chr9:95897200-95898600	Enhancers	GM12878-XiMat	blood
14	chr9:95897200-95898800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr9:95897200-95899200	Enhancers	Brain Anterior Caudate	brain
16	chr9:95897200-95899200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr9:95897200-95899200	Enhancers	Pancreas	Pancrea
18	chr9:95897200-95899400	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr9:95897200-95899400	Enhancers	Placenta	Placenta
20	chr9:95897200-95900200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr9:95897200-95900400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr9:95897200-95900400	Enhancers	Esophagus	oesophagus
23	chr9:95897200-95900400	Enhancers	Fetal Muscle Leg	muscle
24	chr9:95897200-95901000	Enhancers	Brain Cingulate Gyrus	brain
25	chr9:95897200-95902400	Enhancers	Primary B cells from peripheral blood	blood
26	chr9:95897200-95906200	Weak transcription	Right Atrium	heart
27	chr9:95897400-95898600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr9:95897400-95898600	Enhancers	Liver	Liver
29	chr9:95897400-95898600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
30	chr9:95897400-95898600	Enhancers	Duodenum Mucosa	Duodenum
31	chr9:95897400-95898600	Enhancers	Rectal Mucosa Donor 31	rectum
32	chr9:95897400-95898600	Enhancers	HSMM	muscle
33	chr9:95897400-95898600	Enhancers	HSMMtube	muscle
34	chr9:95897400-95899000	Enhancers	Brain Hippocampus Middle	brain
35	chr9:95897400-95900400	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr9:95897400-95900800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
37	chr9:95897400-95901000	Enhancers	Brain Inferior Temporal Lobe	brain
38	chr9:95897400-95906200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr9:95897600-95898600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
40	chr9:95897600-95898600	Enhancers	Adipose Nuclei	Adipose
41	chr9:95897600-95898600	Enhancers	Colonic Mucosa	Colon
42	chr9:95897600-95898600	Enhancers	Duodenum Smooth Muscle	Duodenum
43	chr9:95897600-95898600	Enhancers	Rectal Mucosa Donor 29	rectum
44	chr9:95897600-95898600	Enhancers	Hela-S3	cervix
45	chr9:95897600-95898600	Weak transcription	HUVEC	blood vessel
46	chr9:95897600-95899600	Weak transcription	HMEC	breast
47	chr9:95897600-95900000	Weak transcription	Fetal Intestine Small	intestine
48	chr9:95897600-95900200	Weak transcription	Primary hematopoietic stem cells	blood
49	chr9:95897600-95904600	Weak transcription	Psoas Muscle	Psoas
50	chr9:95897600-95906000	Weak transcription	Sigmoid Colon	Sigmoid Colon

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