Variant report

Variant	rs9299427
Chromosome Location	chr9:97858844-97858845
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:97755782..97758409-chr9:97857933..97859642,2	MCF-7	breast:
2	chr9:97850891..97852903-chr9:97858456..97861126,2	K562	blood:
3	chr9:97676581..97686973-chr9:97850461..97860722,21	MCF-7	breast:
4	chr9:97817856..97820045-chr9:97858304..97860840,2	MCF-7	breast:
5	chr9:97765900..97771029-chr9:97855530..97860219,8	MCF-7	breast:
6	chr9:97851403..97855354-chr9:97856847..97861126,5	K562	blood:
7	chr9:97763635..97773461-chr9:97847821..97861280,36	MCF-7	breast:

Variant related genes	Relation type
ENSG00000148120	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1020962	0.83[ASN][1000 genomes]
rs1038092	0.83[ASN][1000 genomes]
rs10761371	0.83[ASN][1000 genomes]
rs10993471	0.83[ASN][1000 genomes]
rs12555829	0.83[ASN][1000 genomes]
rs1564235	0.83[ASN][1000 genomes]
rs1571896	0.83[ASN][1000 genomes]
rs1623009	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs173339	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1871220	0.83[ASN][1000 genomes]
rs1888944	0.83[ASN][1000 genomes]
rs1888945	0.83[ASN][1000 genomes]
rs1888946	0.83[ASN][1000 genomes]
rs2061798	0.83[ASN][1000 genomes]
rs2061801	0.83[ASN][1000 genomes]
rs2306207	0.83[ASN][1000 genomes]
rs242448	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2655055	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2765817	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs356660	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs356661	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs356662	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs356663	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs356671	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs356685	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs356686	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3739748	0.83[ASN][1000 genomes]
rs3780560	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs400727	0.89[EUR][1000 genomes]
rs4743975	0.83[ASN][1000 genomes]
rs4743977	0.83[ASN][1000 genomes]
rs4743978	0.83[ASN][1000 genomes]
rs4743989	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4744421	0.83[ASN][1000 genomes]
rs4744429	0.83[ASN][1000 genomes]
rs4744437	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4744440	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs475413	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs607105	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs648615	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs651009	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7039768	0.83[ASN][1000 genomes]
rs72750367	0.83[ASN][1000 genomes]
rs72750373	0.83[ASN][1000 genomes]
rs73540087	0.83[ASN][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:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97813000-97873000	Weak transcription	K562	blood
2	chr9:97820600-97875000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr9:97838000-97871200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr9:97841200-97864400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr9:97844000-97898400	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr9:97846000-97861600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr9:97846200-97880000	Weak transcription	Primary B cells from cord blood	blood
8	chr9:97847600-97878400	Weak transcription	Dnd41	blood
9	chr9:97849200-97859200	Weak transcription	Fetal Brain Female	brain
10	chr9:97849200-97863800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr9:97849800-97864600	Enhancers	Psoas Muscle	Psoas
12	chr9:97850000-97862000	Weak transcription	Hela-S3	cervix
13	chr9:97853800-97860400	Weak transcription	Liver	Liver
14	chr9:97854200-97862200	Weak transcription	Aorta	Aorta
15	chr9:97854200-97862200	Weak transcription	HepG2	liver
16	chr9:97854200-97862400	Weak transcription	Primary hematopoietic stem cells	blood
17	chr9:97854800-97860200	Genic enhancers	Stomach Smooth Muscle	stomach
18	chr9:97855000-97867800	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr9:97855200-97859600	Weak transcription	Brain Germinal Matrix	brain
20	chr9:97855200-97876800	Weak transcription	GM12878-XiMat	blood
21	chr9:97855400-97859000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr9:97855400-97860800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr9:97855400-97862200	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr9:97855400-97865400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr9:97855400-97884800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr9:97855600-97859000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr9:97855600-97859600	Weak transcription	Duodenum Mucosa	Duodenum
28	chr9:97855600-97860000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr9:97855600-97862200	Enhancers	Muscle Satellite Cultured Cells	--
30	chr9:97855600-97862400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr9:97855600-97862800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr9:97855600-97863200	Weak transcription	Rectal Smooth Muscle	rectum
33	chr9:97855600-97865400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr9:97855600-97876400	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr9:97855600-97878600	Weak transcription	Stomach Mucosa	stomach
36	chr9:97855800-97860000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr9:97855800-97860000	Strong transcription	NHEK	skin
38	chr9:97855800-97861600	Weak transcription	HMEC	breast
39	chr9:97856200-97860800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr9:97856200-97861000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr9:97856200-97862000	Weak transcription	NHDF-Ad	bronchial
42	chr9:97856200-97862200	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr9:97856200-97862200	Weak transcription	Osteobl	bone
44	chr9:97856200-97872600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr9:97856400-97859000	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr9:97856400-97859200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr9:97856400-97860400	Strong transcription	Fetal Intestine Small	intestine
48	chr9:97856400-97862600	Genic enhancers	Right Ventricle	heart
49	chr9:97856600-97859000	Weak transcription	Fetal Lung	lung
50	chr9:97856600-97859200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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