Variant report

Variant	rs28725394
Chromosome Location	chr9:116104228-116104229
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:21)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:21 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SP1	chr9:116103692-116104672	HCT-116	colon:	n/a	n/a
2	FOSL2	chr9:116103844-116104484	MCF-7	breast:	n/a	n/a
3	JUND	chr9:116103775-116104490	MCF-7	breast:	n/a	chr9:116104160-116104171
4	ELF1	chr9:116103844-116104550	MCF-7	breast:	n/a	n/a
5	FOS	chr9:116104017-116104304	MCF10A-Er-Src	breast:	n/a	n/a
6	BATF	chr9:116104045-116104238	GM12878	blood:	n/a	chr9:116104162-116104173
7	FOS	chr9:116104028-116104302	MCF10A-Er-Src	breast:	n/a	n/a
8	NFIC	chr9:116103892-116104804	ECC-1	luminal epithelium:	n/a	n/a
9	JUND	chr9:116104103-116104268	HepG2	liver:	n/a	chr9:116104160-116104171
10	JUND	chr9:116103792-116104583	HCT-116	colon:	n/a	chr9:116104160-116104171
11	STAT3	chr9:116104102-116104514	MCF10A-Er-Src	breast:	n/a	n/a
12	E2F4	chr9:116104044-116104237	MCF10A-Er-Src	breast:	n/a	n/a
13	FOS	chr9:116104010-116104343	MCF10A-Er-Src	breast:	n/a	n/a
14	POLR2A	chr9:116103897-116104392	HCT-116	colon:	n/a	n/a
15	FOSL2	chr9:116103846-116104488	MCF-7	breast:	n/a	n/a
16	ZNF217	chr9:116103844-116104443	MCF-7	breast:	n/a	n/a
17	NFIC	chr9:116103923-116104801	ECC-1	luminal epithelium:	n/a	n/a
18	JUND	chr9:116104104-116104339	K562	blood:	n/a	chr9:116104160-116104171
19	POLR2A	chr9:116104037-116104294	HCT-116	colon:	n/a	n/a
20	JUND	chr9:116103830-116104516	MCF-7	breast:	n/a	chr9:116104160-116104171
21	FOS	chr9:116103983-116104342	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:116103587..116106029-chr9:116160047..116164950,6	MCF-7	breast:
2	chr9:116102720..116107904-chr9:116161009..116164019,5	MCF-7	breast:
3	chr9:116094633..116097880-chr9:116104158..116105941,3	MCF-7	breast:
4	chr2:232379204..232382044-chr9:116102991..116105023,2	MCF-7	breast:
5	chr9:116103857..116106255-chr9:116138187..116140554,2	MCF-7	breast:
6	chr9:116099899..116105558-chr9:116170913..116174361,7	MCF-7	breast:
7	chr9:116103291..116106183-chr9:116133139..116134993,2	K562	blood:
8	chr9:116063977..116066911-chr9:116102342..116104616,4	MCF-7	breast:
9	chr9:116063284..116065510-chr9:116102338..116105750,4	MCF-7	breast:
10	chr9:116102456..116104363-chr9:116171276..116174227,4	MCF-7	breast:
11	chr9:116036149..116038435-chr9:116101107..116104521,3	K562	blood:
12	chr9:116035986..116039204-chr9:116098421..116104240,5	MCF-7	breast:

No data

Variant related genes	Relation type
WDR31	TF binding region
ENSG00000176386	Chromatin interaction
ENSG00000165188	Chromatin interaction
ENSG00000148229	Chromatin interaction
ENSG00000119431	Chromatin interaction
ENSG00000157653	Chromatin interaction
ENSG00000148218	Chromatin interaction
ENSG00000136875	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10114352	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10118304	1.00[AMR][1000 genomes]
rs10120336	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10122035	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10481672	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10481673	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10481675	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10981753	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12336439	0.85[AMR][1000 genomes]
rs12337069	0.85[AMR][1000 genomes]
rs12337123	0.85[AMR][1000 genomes]
rs12339006	0.85[AMR][1000 genomes]
rs12345499	0.85[AMR][1000 genomes]
rs12346510	0.85[AMR][1000 genomes]
rs12347798	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12348236	0.85[AMR][1000 genomes]
rs12348581	0.85[AMR][1000 genomes]
rs12350255	0.85[AMR][1000 genomes]
rs12350332	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12350377	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12352852	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12352895	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28375224	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28393902	1.00[AMR][1000 genomes]
rs28488898	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28536744	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28556819	0.85[AMR][1000 genomes]
rs28597401	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7850003	0.92[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv1042663	chr9:115920158-116167140	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv893744	chr9:115934852-116170227	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116102800-116104600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr9:116102800-116105800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr9:116103000-116104600	Enhancers	Primary T cells fromperipheralblood	blood
4	chr9:116103000-116105600	Weak transcription	Left Ventricle	heart
5	chr9:116103000-116106200	Weak transcription	Esophagus	oesophagus
6	chr9:116103000-116107200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr9:116103000-116111800	Weak transcription	Lung	lung
8	chr9:116103200-116104600	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr9:116103200-116104600	Weak transcription	Psoas Muscle	Psoas
10	chr9:116103200-116104600	Enhancers	Rectal Mucosa Donor 31	rectum
11	chr9:116103200-116104800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr9:116103200-116104800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr9:116103200-116104800	Enhancers	HMEC	breast
14	chr9:116103200-116105000	Weak transcription	Right Ventricle	heart
15	chr9:116103200-116105200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr9:116103200-116105400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr9:116103200-116105600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr9:116103200-116105600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr9:116103200-116105600	Weak transcription	Brain Anterior Caudate	brain
20	chr9:116103200-116105600	Weak transcription	Brain Cingulate Gyrus	brain
21	chr9:116103200-116105600	Weak transcription	Brain Substantia Nigra	brain
22	chr9:116103200-116105600	Weak transcription	Colon Smooth Muscle	Colon
23	chr9:116103200-116105600	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr9:116103200-116105800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr9:116103200-116105800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr9:116103200-116105800	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr9:116103200-116105800	Weak transcription	Fetal Intestine Small	intestine
28	chr9:116103200-116105800	Weak transcription	Fetal Lung	lung
29	chr9:116103200-116105800	Weak transcription	Fetal Muscle Leg	muscle
30	chr9:116103200-116105800	Weak transcription	NHDF-Ad	bronchial
31	chr9:116103200-116106000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr9:116103200-116106200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr9:116103200-116106200	Weak transcription	Colonic Mucosa	Colon
34	chr9:116103200-116106400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr9:116103200-116106400	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr9:116103200-116107000	Weak transcription	Duodenum Mucosa	Duodenum
37	chr9:116103200-116107200	Weak transcription	Brain Angular Gyrus	brain
38	chr9:116103200-116107400	Weak transcription	Fetal Intestine Large	intestine
39	chr9:116103200-116108000	Enhancers	Fetal Heart	heart
40	chr9:116103200-116108200	Enhancers	Cortex derived primary cultured neurospheres	brain
41	chr9:116103200-116108600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr9:116103200-116108800	Weak transcription	Placenta	Placenta
43	chr9:116103200-116110000	Weak transcription	Right Atrium	heart
44	chr9:116103200-116111400	Weak transcription	Stomach Mucosa	stomach
45	chr9:116103200-116111400	Weak transcription	GM12878-XiMat	blood
46	chr9:116103400-116104600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr9:116103400-116105400	Weak transcription	Brain Hippocampus Middle	brain
48	chr9:116103400-116105600	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr9:116103400-116105800	Weak transcription	Liver	Liver
50	chr9:116103400-116105800	Weak transcription	Skeletal Muscle Female	skeletal muscle

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