Variant report

Variant	rs9330310
Chromosome Location	chr2:110265558-110265559
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:110265348..110267914-chr2:110269855..110271793,2	MCF-7	breast:
2	chr2:110261068..110263464-chr2:110265348..110267401,2	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10175432	0.84[ASN][1000 genomes]
rs11541143	0.87[CHB][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap];0.91[TSI][hapmap]
rs12998808	0.86[ASN][1000 genomes]
rs2043462	0.83[CHB][hapmap];0.91[JPT][hapmap];0.86[TSI][hapmap]
rs2060403	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs3923006	0.82[ASN][1000 genomes]
rs3934873	0.84[ASN][1000 genomes]
rs4953760	0.83[CHB][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap];0.89[TSI][hapmap]
rs4953784	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs4953843	0.91[JPT][hapmap];0.86[TSI][hapmap]
rs6594037	0.83[CHB][hapmap];0.91[JPT][hapmap];0.89[TSI][hapmap]
rs6594049	0.81[JPT][hapmap]
rs6723295	0.83[CHB][hapmap];0.91[JPT][hapmap];0.86[TSI][hapmap]
rs919941	0.91[JPT][hapmap]
rs9330311	0.90[ASN][1000 genomes]
rs9330320	0.84[ASN][1000 genomes]
rs9330324	0.81[ASN][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	nsv874777	chr2:109825516-110693317	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv874779	chr2:110030964-110270250	Enhancers Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv874780	chr2:110078080-110432886	Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9330310	SEPT10	cis	Muscle Skeletal	GTEx
rs9330310	SEPT10	cis	multi-tissue	Pritchard
rs9330310	SEPT10	cis	parietal	SCAN
rs9330310	C2orf26	cis	multi-tissue	Pritchard
rs9330310	MALL	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:110256200-110270800	Weak transcription	Esophagus	oesophagus
2	chr2:110256200-110270800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr2:110256200-110271400	Weak transcription	Ovary	ovary
4	chr2:110257800-110287800	Weak transcription	Gastric	stomach
5	chr2:110258200-110271200	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr2:110259600-110267600	Weak transcription	NHLF	lung
7	chr2:110261600-110271200	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr2:110262000-110266400	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr2:110262400-110267600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr2:110262800-110270400	Weak transcription	Right Ventricle	heart
11	chr2:110263800-110266000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr2:110263800-110266600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr2:110263800-110267600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr2:110263800-110268200	Weak transcription	Brain Germinal Matrix	brain
15	chr2:110263800-110271000	Weak transcription	Colon Smooth Muscle	Colon
16	chr2:110264000-110267600	Weak transcription	Fetal Brain Male	brain
17	chr2:110264200-110266800	Enhancers	Primary hematopoietic stem cells	blood
18	chr2:110264200-110268400	Weak transcription	Fetal Brain Female	brain
19	chr2:110264400-110265600	Enhancers	GM12878-XiMat	blood
20	chr2:110264400-110266600	Enhancers	Placenta	Placenta
21	chr2:110265000-110266200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr2:110265200-110265600	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr2:110265200-110265800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr2:110265400-110265600	Enhancers	Fetal Kidney	kidney
25	chr2:110265400-110265800	Enhancers	Skeletal Muscle Female	skeletal muscle

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