Variant report

Variant	rs2297644
Chromosome Location	chr10:99359739-99359740
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:99256903..99258777-chr10:99359333..99362265,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155229	Chromatin interaction
ENSG00000165886	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10882954	1.00[CHB][hapmap]
rs11540693	1.00[ASN][1000 genomes]
rs11817730	0.87[CEU][hapmap]
rs61863282	0.83[EUR][1000 genomes]
rs7068278	0.87[CEU][hapmap]
rs7070104	1.00[CHB][hapmap];0.83[CHD][hapmap]
rs7078003	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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	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

Variant related diseases (count:1)

Disease	PMID	Source
Metabolite levels	22286219	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2297644	FRAT2	cis	cerebellum	SCAN
rs2297644	MORN4	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:99349600-99370800	Weak transcription	Fetal Stomach	stomach
2	chr10:99350600-99360600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr10:99350800-99361600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr10:99351600-99375600	Weak transcription	Fetal Intestine Small	intestine
5	chr10:99356400-99360400	Weak transcription	Fetal Muscle Leg	muscle
6	chr10:99356400-99360800	Enhancers	Skeletal Muscle Male	skeletal muscle
7	chr10:99356400-99361400	Weak transcription	Fetal Muscle Trunk	muscle
8	chr10:99356400-99361600	Weak transcription	Aorta	Aorta
9	chr10:99356400-99373800	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr10:99356600-99361200	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr10:99356800-99366200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr10:99357000-99366200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr10:99357400-99361200	Weak transcription	HSMM	muscle
14	chr10:99357400-99361800	Enhancers	Left Ventricle	heart
15	chr10:99357600-99360800	Weak transcription	Brain Substantia Nigra	brain
16	chr10:99357600-99361400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr10:99357800-99360800	Weak transcription	NHLF	lung
18	chr10:99357800-99367000	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr10:99357800-99367000	Weak transcription	Right Atrium	heart
20	chr10:99358000-99361600	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr10:99358200-99362800	Strong transcription	Liver	Liver
22	chr10:99358400-99361400	Weak transcription	A549	lung
23	chr10:99358600-99360000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr10:99358800-99371200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr10:99359000-99360800	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr10:99359000-99368400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr10:99359200-99375600	Weak transcription	Pancreas	Pancrea
28	chr10:99359400-99375600	Weak transcription	Fetal Intestine Large	intestine
29	chr10:99359600-99360000	Weak transcription	Fetal Heart	heart
30	chr10:99359600-99360800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr10:99359600-99361400	Enhancers	Psoas Muscle	Psoas
32	chr10:99359600-99370000	Weak transcription	Right Ventricle	heart

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