Variant report

Variant	rs296894
Chromosome Location	chr9:86598444-86598445
allele	A/C
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	IRF1	chr9:86598438-86598477	K562	blood:	n/a	n/a
2	STAT3	chr9:86598287-86598598	MCF10A-Er-Src	breast:	n/a	chr9:86598309-86598317
3	GATA3	chr9:86598435-86598837	SH-SY5Y	brain:	n/a	chr9:86598659-86598672
4	IRF1	chr9:86598418-86598701	K562	blood:	n/a	chr9:86598632-86598641

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:86320289..86324589-chr9:86593742..86599530,6	K562	blood:
2	chr9:86533593..86537892-chr9:86593047..86598677,10	K562	blood:

Variant related genes	Relation type
HNRNPK	TF binding region
ENSG00000254473	Chromatin interaction
ENSG00000165115	Chromatin interaction
ENSG00000135018	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10746729	0.86[EUR][1000 genomes]
rs10780643	0.86[EUR][1000 genomes]
rs10780644	0.86[EUR][1000 genomes]
rs10780645	0.93[CEU][hapmap];0.97[GIH][hapmap];0.89[MEX][hapmap];0.89[TSI][hapmap]
rs13295313	0.84[EUR][1000 genomes]
rs167203	0.93[CEU][hapmap];0.86[EUR][1000 genomes]
rs1982151	0.81[CEU][hapmap]
rs28521174	0.84[EUR][1000 genomes]
rs296886	0.93[CEU][hapmap];0.84[GIH][hapmap];0.89[MEX][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs296887	0.81[CEU][hapmap]
rs296888	0.81[CEU][hapmap]
rs296889	0.81[CEU][hapmap]
rs296893	0.81[CEU][hapmap]
rs6559742	0.86[CEU][hapmap]
rs7033292	0.81[CEU][hapmap]
rs7853235	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs7853377	0.93[CEU][hapmap];0.83[EUR][1000 genomes]
rs930340	1.00[CEU][hapmap];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758192	chr9:86414024-86603602	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
2	esv2759701	chr9:86414024-86603602	Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
3	nsv831644	chr9:86534310-86704395	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
4	esv3366490	chr9:86541369-86608868	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
5	nsv1043703	chr9:86545917-86603545	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
6	nsv893514	chr9:86584160-86678917	Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs296894	LOC440173	cis	parietal	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86593000-86598600	Active TSS	GM12878-XiMat	blood
2	chr9:86596400-86632400	Weak transcription	Spleen	Spleen
3	chr9:86596600-86601800	Weak transcription	Pancreas	Pancrea
4	chr9:86596600-86603200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr9:86596600-86610600	Weak transcription	Esophagus	oesophagus
6	chr9:86596600-86613400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr9:86596600-86613800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr9:86596600-86616000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr9:86596600-86617000	Weak transcription	Lung	lung
10	chr9:86596600-86618200	Weak transcription	Ovary	ovary
11	chr9:86596600-86619600	Weak transcription	Gastric	stomach
12	chr9:86596800-86601200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr9:86596800-86601200	Weak transcription	Liver	Liver
14	chr9:86596800-86601800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr9:86596800-86601800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr9:86596800-86601800	Weak transcription	Left Ventricle	heart
17	chr9:86596800-86601800	Weak transcription	HSMM	muscle
18	chr9:86596800-86602000	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr9:86596800-86603200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr9:86596800-86603200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr9:86596800-86603200	Weak transcription	Fetal Thymus	thymus
22	chr9:86596800-86605400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr9:86596800-86606600	Weak transcription	Rectal Smooth Muscle	rectum
24	chr9:86596800-86613200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr9:86596800-86614400	Weak transcription	HSMMtube	muscle
26	chr9:86596800-86616000	Weak transcription	Brain Hippocampus Middle	brain
27	chr9:86596800-86616200	Weak transcription	Brain Angular Gyrus	brain
28	chr9:86596800-86616200	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr9:86596800-86619600	Weak transcription	Small Intestine	intestine
30	chr9:86596800-86621400	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr9:86596800-86621600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr9:86597000-86598600	Flanking Active TSS	Dnd41	blood
33	chr9:86597000-86598800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr9:86597000-86598800	Enhancers	Hela-S3	cervix
35	chr9:86597000-86600400	Weak transcription	Duodenum Mucosa	Duodenum
36	chr9:86597000-86600600	Weak transcription	Primary B cells from peripheral blood	blood
37	chr9:86597000-86601000	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr9:86597000-86601200	Weak transcription	Osteobl	bone
39	chr9:86597000-86601400	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr9:86597000-86602000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr9:86597000-86602800	Weak transcription	Fetal Intestine Small	intestine
42	chr9:86597000-86603200	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr9:86597000-86603200	Weak transcription	Fetal Muscle Leg	muscle
44	chr9:86597000-86603400	Weak transcription	Fetal Intestine Large	intestine
45	chr9:86597000-86603600	Weak transcription	Thymus	Thymus
46	chr9:86597000-86609600	Weak transcription	Primary T cells from cord blood	blood
47	chr9:86597000-86614200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr9:86597000-86616000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr9:86597000-86616000	Weak transcription	Fetal Lung	lung
50	chr9:86597000-86617200	Weak transcription	Primary T helper cells fromperipheralblood	blood

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