Variant report

Variant	rs17322612
Chromosome Location	chr10:89876255-89876256
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:89875899..89878247-chr10:89928354..89931128,2	MCF-7	breast:
2	chr10:89874131..89877304-chr10:89878864..89883197,3	MCF-7	breast:
3	chr10:89872459..89874892-chr10:89876051..89878099,2	K562	blood:
4	chr10:89874980..89876628-chr10:89878193..89879862,2	K562	blood:
5	chr10:89620841..89625888-chr10:89873162..89876316,7	MCF-7	breast:
6	chr10:89620141..89628673-chr10:89867993..89880509,31	MCF-7	breast:
7	chr10:89871797..89873959-chr10:89875999..89877551,2	K562	blood:

Variant related genes	Relation type
ENSG00000227268	Chromatin interaction
ENSG00000171862	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11593673	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12573738	0.80[EUR][1000 genomes]
rs17322521	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17419930	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2225796	0.96[CEU][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55722339	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55727359	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56375327	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7079675	0.81[EUR][1000 genomes]
rs72816194	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7899035	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7905605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831940	chr10:89811247-89989199	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17322612	LRIT2	cis	parietal	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:89868400-89876800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr10:89869600-89881400	Enhancers	Primary B cells from peripheral blood	blood
3	chr10:89872200-89878800	Enhancers	Fetal Thymus	thymus
4	chr10:89872400-89881200	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr10:89872600-89877800	Enhancers	Primary hematopoietic stem cells	blood
6	chr10:89872600-89878200	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr10:89872600-89878200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr10:89872800-89877400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr10:89872800-89878800	Enhancers	Primary T cells from cord blood	blood
10	chr10:89873200-89878200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr10:89873800-89879000	Weak transcription	Duodenum Mucosa	Duodenum
12	chr10:89874000-89877800	Weak transcription	Adipose Nuclei	Adipose
13	chr10:89874000-89878000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr10:89874000-89880200	Weak transcription	Right Atrium	heart
15	chr10:89874000-89881200	Enhancers	Primary B cells from cord blood	blood
16	chr10:89874000-89891400	Weak transcription	Left Ventricle	heart
17	chr10:89874200-89877800	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr10:89874200-89878600	Weak transcription	Stomach Mucosa	stomach
19	chr10:89874600-89876600	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr10:89874600-89876600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr10:89874600-89877000	Weak transcription	Spleen	Spleen
22	chr10:89874600-89877200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr10:89874600-89878000	Weak transcription	Liver	Liver
24	chr10:89874600-89878800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
25	chr10:89874600-89879800	Weak transcription	Lung	lung
26	chr10:89874600-89880800	Weak transcription	Fetal Muscle Leg	muscle
27	chr10:89874600-89882400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr10:89874800-89877800	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr10:89874800-89877800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr10:89875200-89876800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr10:89875200-89879200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr10:89875400-89876400	Enhancers	Hela-S3	cervix
33	chr10:89875400-89877200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr10:89875400-89877200	Enhancers	NH-A	brain
35	chr10:89875400-89877200	Enhancers	NHLF	lung
36	chr10:89875400-89877400	Enhancers	Muscle Satellite Cultured Cells	--
37	chr10:89875400-89877400	Enhancers	HMEC	breast
38	chr10:89875400-89877400	Enhancers	NHEK	skin
39	chr10:89875400-89877800	Enhancers	Osteobl	bone
40	chr10:89875400-89878200	Enhancers	Thymus	Thymus
41	chr10:89875400-89878600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr10:89875400-89879000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr10:89875400-89879000	Enhancers	HSMMtube	muscle
44	chr10:89875600-89877000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr10:89875600-89877000	Enhancers	NHDF-Ad	bronchial
46	chr10:89875600-89877600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr10:89875600-89878000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr10:89876000-89876800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr10:89876000-89876800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
50	chr10:89876000-89878000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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