Variant report

Variant	rs2282373
Chromosome Location	chr10:99343081-99343082
allele	C/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	CTCF	chr10:99343040-99343190	GM12872	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:99341781..99343970-chr10:99356673..99358698,2	MCF-7	breast:
2	chr10:99329733..99337149-chr10:99338392..99346753,19	MCF-7	breast:
3	chr10:99342912..99345937-chr10:99348140..99351473,3	K562	blood:
4	chr10:99331113..99332849-chr10:99340895..99343387,2	MCF-7	breast:

Variant related genes	Relation type
HOGA1	TF binding region
PI4K2A	TF binding region
ENSG00000249967	TF binding region
ENSG00000165887	Chromatin interaction
ENSG00000203942	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10748699	0.80[CEU][hapmap]
rs10882959	0.80[CEU][hapmap]
rs10882962	0.80[CEU][hapmap]
rs10882963	0.80[CEU][hapmap]
rs11189275	0.80[CEU][hapmap]
rs11189284	0.80[CEU][hapmap]
rs1572860	0.80[CEU][hapmap]
rs2282372	0.94[ASW][hapmap];0.90[CEU][hapmap];0.89[GIH][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];0.80[TSI][hapmap];0.81[YRI][hapmap];0.89[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs3818910	0.80[CEU][hapmap]
rs7342022	0.80[EUR][1000 genomes]
rs7902642	0.80[CEU][hapmap]

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	esv1817777	chr10:99196035-99558169	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv1036494	chr10:99267639-99345207	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
3	nsv1047359	chr10:99306501-99369013	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
4	nsv818782	chr10:99337572-99350128	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
5	nsv971896	chr10:99338341-99349551	Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2282373	RRP12	cis	parietal	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:99334800-99343400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr10:99335000-99343400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr10:99335200-99343400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr10:99336000-99348800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr10:99336200-99343400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr10:99336200-99343400	Weak transcription	Psoas Muscle	Psoas
7	chr10:99338400-99343400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr10:99338400-99343800	Weak transcription	Lung	lung
9	chr10:99338600-99343800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr10:99338800-99343200	Weak transcription	Fetal Muscle Leg	muscle
11	chr10:99338800-99343400	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr10:99340000-99343600	Genic enhancers	Skeletal Muscle Male	skeletal muscle
13	chr10:99340400-99344400	Weak transcription	Pancreas	Pancrea
14	chr10:99340600-99343600	Weak transcription	Placenta	Placenta
15	chr10:99340600-99343600	Weak transcription	Hela-S3	cervix
16	chr10:99341200-99343400	Weak transcription	Right Atrium	heart
17	chr10:99341400-99343400	Weak transcription	Adipose Nuclei	Adipose
18	chr10:99342000-99343400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr10:99342400-99344200	Enhancers	Left Ventricle	heart
20	chr10:99342600-99343200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr10:99342600-99344000	Weak transcription	Gastric	stomach
22	chr10:99342600-99345200	Enhancers	Fetal Muscle Trunk	muscle
23	chr10:99342800-99343400	Weak transcription	Right Ventricle	heart
24	chr10:99342800-99343800	Weak transcription	Spleen	Spleen
25	chr10:99343000-99343600	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr10:99343000-99343600	Enhancers	A549	lung
27	chr10:99343000-99344000	Enhancers	Brain Substantia Nigra	brain
28	chr10:99343000-99344200	Enhancers	Liver	Liver
29	chr10:99343000-99346600	Enhancers	Fetal Heart	heart

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