Variant report

Variant	rs57883597
Chromosome Location	chr9:97850729-97850730
allele	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	BCL3	chr9:97849652-97856909	A549	lung:	n/a	chr9:97849910-97849923 chr9:97856480-97856489 chr9:97852058-97852071
2	TCF12	chr9:97849698-97856389	A549	lung:	n/a	chr9:97854161-97854171 chr9:97855868-97855877 chr9:97853824-97853834
3	POLR2A	chr9:97850725-97850977	A549	lung:	n/a	n/a
4	POLR2A	chr9:97850706-97851457	A549	lung:	n/a	n/a
5	POLR2A	chr9:97850695-97854293	A549	lung:	n/a	n/a
6	POLR2A	chr9:97849710-97856872	A549	lung:	n/a	n/a
7	POLR2A	chr9:97850515-97850835	HepG2	liver:	n/a	n/a
8	JUND	chr9:97850694-97855193	A549	lung:	n/a	chr9:97851092-97851101 chr9:97854992-97855000 chr9:97851091-97851101 chr9:97851091-97851101 chr9:97854990-97855002 chr9:97851091-97851101 chr9:97851091-97851101 chr9:97853499-97853510 chr9:97851088-97851099
9	BCL3	chr9:97850692-97856305	A549	lung:	n/a	chr9:97852058-97852071
10	POLR2A	chr9:97850684-97855827	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:97542830..97545595-chr9:97848570..97851188,3	MCF-7	breast:
2	chr9:97848613..97851879-chr9:97854740..97857228,3	K562	blood:
3	chr9:97846609..97848201-chr9:97850195..97853098,2	K562	blood:
4	chr9:97682387..97688736-chr9:97850073..97858737,16	MCF-7	breast:
5	chr9:97676581..97686973-chr9:97850461..97860722,21	MCF-7	breast:
6	chr2:39220003..39220567-chr9:97850457..97851397,2	MCF-7	breast:
7	chr9:97763635..97773461-chr9:97847821..97861280,36	MCF-7	breast:

Variant related genes	Relation type
MIR3074	TF binding region
ENSG00000207864	Chromatin interaction
ENSG00000148120	Chromatin interaction
ENSG00000207563	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10453242	0.87[AFR][1000 genomes]
rs55651673	0.87[AFR][1000 genomes]
rs56025140	0.87[AFR][1000 genomes]
rs56134011	0.87[AFR][1000 genomes]
rs56280046	1.00[AFR][1000 genomes]
rs56737425	1.00[AFR][1000 genomes]
rs56761320	0.87[AFR][1000 genomes]
rs57312263	1.00[AFR][1000 genomes]
rs59611901	1.00[AFR][1000 genomes]
rs60346856	0.87[AFR][1000 genomes]
rs61462331	0.87[AFR][1000 genomes]
rs73654524	1.00[AFR][1000 genomes]
rs73654529	1.00[AFR][1000 genomes]
rs73654531	1.00[AFR][1000 genomes]
rs73654532	1.00[AFR][1000 genomes]
rs73654534	0.87[AFR][1000 genomes]
rs73654535	0.87[AFR][1000 genomes]
rs73654536	0.87[AFR][1000 genomes]
rs73654537	0.87[AFR][1000 genomes]
rs73654538	0.87[AFR][1000 genomes]
rs73654540	0.87[AFR][1000 genomes]
rs73654542	1.00[AFR][1000 genomes]
rs73654543	0.87[AFR][1000 genomes]
rs73654544	0.87[AFR][1000 genomes]

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	nsv933919	chr9:97619512-97919344	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	293 gene(s)	inside rSNPs	diseases
2	nsv1038106	chr9:97793038-97881416	Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
3	nsv1038523	chr9:97797032-97923774	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
4	nsv540175	chr9:97797032-97923774	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
5	nsv831656	chr9:97831551-97989980	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97813000-97873000	Weak transcription	K562	blood
2	chr9:97820000-97854200	Weak transcription	Fetal Brain Male	brain
3	chr9:97820600-97875000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr9:97825400-97854400	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr9:97825800-97852600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr9:97838000-97871200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr9:97839600-97851000	Genic enhancers	A549	lung
8	chr9:97840800-97851800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr9:97841200-97864400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr9:97841400-97853000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr9:97841600-97855000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr9:97841800-97851600	Strong transcription	Fetal Intestine Small	intestine
13	chr9:97841800-97853800	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr9:97841800-97854000	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr9:97842200-97852000	Strong transcription	NHEK	skin
16	chr9:97842400-97852600	Strong transcription	Fetal Intestine Large	intestine
17	chr9:97842400-97854200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr9:97842800-97850800	Strong transcription	Placenta	Placenta
19	chr9:97843200-97851600	Strong transcription	Placenta Amnion	Placenta Amnion
20	chr9:97843200-97851800	Genic enhancers	Brain Hippocampus Middle	brain
21	chr9:97843200-97852400	Genic enhancers	Rectal Smooth Muscle	rectum
22	chr9:97843600-97853400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr9:97844000-97854800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr9:97844000-97898400	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr9:97844400-97852200	Strong transcription	Fetal Stomach	stomach
26	chr9:97844400-97854200	Weak transcription	Brain Germinal Matrix	brain
27	chr9:97845000-97852600	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr9:97845800-97854400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr9:97845800-97854400	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr9:97846000-97850800	Weak transcription	Right Atrium	heart
31	chr9:97846000-97853000	Weak transcription	Fetal Kidney	kidney
32	chr9:97846000-97853200	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr9:97846000-97853800	Weak transcription	GM12878-XiMat	blood
34	chr9:97846000-97861600	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr9:97846200-97851200	Strong transcription	Duodenum Mucosa	Duodenum
36	chr9:97846200-97853400	Weak transcription	Small Intestine	intestine
37	chr9:97846200-97853600	Weak transcription	Primary hematopoietic stem cells	blood
38	chr9:97846200-97880000	Weak transcription	Primary B cells from cord blood	blood
39	chr9:97847000-97852600	Genic enhancers	Colon Smooth Muscle	Colon
40	chr9:97847000-97853600	Genic enhancers	Muscle Satellite Cultured Cells	--
41	chr9:97847200-97851800	Genic enhancers	Esophagus	oesophagus
42	chr9:97847200-97852800	Genic enhancers	HSMM	muscle
43	chr9:97847200-97853200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr9:97847200-97854000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr9:97847400-97853600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr9:97847600-97852400	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr9:97847600-97852400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr9:97847600-97853800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr9:97847600-97878400	Weak transcription	Dnd41	blood
50	chr9:97847800-97851400	Enhancers	Brain Substantia Nigra	brain

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