Variant report

Variant	rs28688962
Chromosome Location	chr9:108053691-108053692
allele	A/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	ELF1	chr9:108053653-108054054	HepG2	liver:	n/a	n/a
2	CEBPB	chr9:108053683-108054181	HepG2	liver:	n/a	chr9:108053879-108053890
3	POLR2A	chr9:108053557-108053885	HepG2	liver:	n/a	n/a
4	HNF4A	chr9:108053623-108054082	HepG2	liver:	n/a	chr9:108053908-108053920 chr9:108053906-108053921
5	HNF4A	chr9:108053625-108054124	HepG2	liver:	n/a	chr9:108053908-108053920 chr9:108053906-108053921
6	FOXA1	chr9:108053586-108054111	HepG2	liver:	n/a	n/a
7	TEAD4	chr9:108053434-108054248	HepG2	liver:	n/a	n/a
8	ARID3A	chr9:108052906-108054144	HepG2	liver:	n/a	n/a
9	FOXA1	chr9:108053567-108054000	HepG2	liver:	n/a	n/a
10	CEBPB	chr9:108053602-108054092	A549	lung:	n/a	chr9:108053879-108053890
11	FOXA2	chr9:108053520-108053997	HepG2	liver:	n/a	n/a
12	HEY1	chr9:108053515-108054100	HepG2	liver:	n/a	n/a
13	JUND	chr9:108053617-108054048	HepG2	liver:	n/a	n/a
14	RXRA	chr9:108053663-108054069	HepG2	liver:	n/a	chr9:108053685-108053694
15	CEBPB	chr9:108053637-108054018	HepG2	liver:	n/a	chr9:108053879-108053890
16	RAD21	chr9:108053573-108054125	HepG2	liver:	n/a	n/a
17	MYBL2	chr9:108053608-108054282	HepG2	liver:	n/a	n/a
18	RAD21	chr9:108053612-108053990	HepG2	liver:	n/a	n/a
19	SMC3	chr9:108053599-108054057	HepG2	liver:	n/a	n/a
20	HDAC2	chr9:108053546-108054111	HepG2	liver:	n/a	n/a
21	ELF1	chr9:108053580-108054034	HepG2	liver:	n/a	n/a
22	JUN	chr9:108053466-108054079	HepG2	liver:	n/a	n/a
23	MBD4	chr9:108053455-108054099	HepG2	liver:	n/a	n/a
24	NFIC	chr9:108053485-108054182	HepG2	liver:	n/a	n/a
25	HNF4A	chr9:108053657-108054061	HepG2	liver:	n/a	chr9:108053908-108053920 chr9:108053906-108053921
26	MYBL2	chr9:108053387-108054225	HepG2	liver:	n/a	n/a
27	TEAD4	chr9:108053691-108054038	HepG2	liver:	n/a	n/a
28	EP300	chr9:108053507-108054147	HepG2	liver:	n/a	n/a
29	RCOR1	chr9:108053690-108054079	HepG2	liver:	n/a	n/a
30	POLR2A	chr9:108053624-108053793	MCF10A-Er-Src	breast:	n/a	n/a
31	NR3C1	chr9:108053591-108054064	A549	lung:	n/a	n/a
32	CEBPB	chr9:108053516-108054290	HepG2	liver:	n/a	chr9:108054273-108054284 chr9:108053879-108053890
33	HNF4G	chr9:108053606-108054070	HepG2	liver:	n/a	chr9:108053908-108053920
34	JUND	chr9:108053588-108054038	HepG2	liver:	n/a	n/a
35	FOXA1	chr9:108053555-108054142	HepG2	liver:	n/a	n/a
36	REST	chr9:108053632-108054054	HepG2	liver:	n/a	chr9:108053688-108053697
37	HDAC2	chr9:108053535-108054102	HepG2	liver:	n/a	n/a
38	EP300	chr9:108053687-108054081	HepG2	liver:	n/a	n/a
39	EP300	chr9:108053406-108054141	HepG2	liver:	n/a	n/a
40	HEY1	chr9:108053610-108053972	HepG2	liver:	n/a	n/a
41	SP1	chr9:108053538-108054128	HepG2	liver:	n/a	chr9:108053854-108053864 chr9:108053854-108053863 chr9:108053853-108053865
42	FOXA1	chr9:108053519-108054143	HepG2	liver:	n/a	n/a
43	NFIC	chr9:108053609-108054121	HepG2	liver:	n/a	n/a
44	REST	chr9:108053639-108053950	HepG2	liver:	n/a	chr9:108053688-108053697

No.	Distal block	Cell Line	Cell type
1	chr9:108052363..108054677-chr9:108071523..108074219,3	MCF-7	breast:
2	chr9:108005087..108008498-chr9:108050324..108055404,7	MCF-7	breast:
3	chr9:108053038..108054954-chr9:108056839..108058571,2	K562	blood:
4	chr9:108052475..108054719-chr9:108057760..108060481,3	MCF-7	breast:
5	chr9:108051884..108054784-chr9:108055791..108058847,3	MCF-7	breast:
6	chr9:108053113..108055212-chr9:108060978..108062866,2	MCF-7	breast:

Variant related genes	Relation type
SLC44A1	TF binding region
ENSG00000070214	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs12341869	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57877883	1.00[AMR][1000 genomes]
rs59290851	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6479300	0.90[AFR][1000 genomes]
rs6479301	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6479302	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6479303	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6479304	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7024012	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7026389	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7033929	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7039638	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7046185	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7048497	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72744219	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs72744225	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73510211	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73510218	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73510246	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73510280	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73510281	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73510289	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73510295	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73666622	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73666624	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73666625	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7847744	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7847952	0.84[AFR][1000 genomes]
rs7853038	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7853709	0.83[AMR][1000 genomes]
rs7854064	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7854282	1.00[AMR][1000 genomes]
rs7857088	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7860356	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7869261	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7873924	0.83[AMR][1000 genomes]
rs7874307	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9777083	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045108	chr9:107509553-108188550	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv831678	chr9:107923522-108112813	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv893685	chr9:107940737-108083485	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv893686	chr9:107968330-108083485	Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv893687	chr9:107973277-108083485	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv893688	chr9:107974761-108083485	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv893689	chr9:107978563-108130606	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv893690	chr9:107992706-108083485	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv1037750	chr9:108027692-108251733	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108033200-108056200	Weak transcription	Primary T cells from cord blood	blood
2	chr9:108043600-108057400	Weak transcription	HSMM	muscle
3	chr9:108043600-108059400	Weak transcription	NHLF	lung
4	chr9:108043600-108059800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr9:108044800-108056600	Weak transcription	Hela-S3	cervix
6	chr9:108049400-108074200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr9:108049800-108057400	Enhancers	Brain Inferior Temporal Lobe	brain
8	chr9:108050200-108054800	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr9:108050200-108061400	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr9:108050200-108061800	Weak transcription	Fetal Stomach	stomach
11	chr9:108050600-108056000	Enhancers	Placenta	Placenta
12	chr9:108051000-108057800	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr9:108051000-108061600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr9:108051200-108055000	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr9:108051400-108056600	Enhancers	Brain Hippocampus Middle	brain
16	chr9:108052000-108054000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr9:108052000-108054200	Enhancers	Fetal Intestine Large	intestine
18	chr9:108052200-108054200	Enhancers	NHEK	skin
19	chr9:108052400-108054000	Enhancers	Fetal Intestine Small	intestine
20	chr9:108052400-108054200	Enhancers	Stomach Mucosa	stomach
21	chr9:108052400-108054400	Enhancers	HMEC	breast
22	chr9:108052400-108054600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr9:108052400-108054600	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr9:108052400-108054600	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr9:108052400-108056600	Enhancers	Brain Angular Gyrus	brain
26	chr9:108052400-108061400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr9:108052600-108055400	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr9:108052600-108058200	Enhancers	iPS-15b Cell Line	embryonic stem cell
29	chr9:108052600-108058200	Enhancers	iPS-18 Cell Line	embryonic stem cell
30	chr9:108052800-108053800	Enhancers	Duodenum Mucosa	Duodenum
31	chr9:108052800-108054000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr9:108052800-108054000	Enhancers	Muscle Satellite Cultured Cells	--
33	chr9:108052800-108054200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr9:108052800-108054200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr9:108052800-108054400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr9:108052800-108054400	Flanking Active TSS	HepG2	liver
37	chr9:108052800-108054400	Enhancers	Monocytes-CD14+_RO01746	blood
38	chr9:108052800-108054800	Enhancers	Liver	Liver
39	chr9:108052800-108054800	Enhancers	Fetal Lung	lung
40	chr9:108052800-108055200	Enhancers	ES-I3 Cell Line	embryonic stem cell
41	chr9:108052800-108055800	Enhancers	HUES6 Cell Line	embryonic stem cell
42	chr9:108052800-108056400	Enhancers	Brain Cingulate Gyrus	brain
43	chr9:108052800-108056600	Enhancers	Brain Anterior Caudate	brain
44	chr9:108052800-108058000	Enhancers	HUES64 Cell Line	embryonic stem cell
45	chr9:108052800-108061400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr9:108053000-108054000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr9:108053000-108054000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr9:108053000-108054200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr9:108053000-108054600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr9:108053000-108056000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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