Variant report

Variant	rs13005010
Chromosome Location	chr2:173259273-173259274
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12992315	0.81[EUR][1000 genomes]
rs12996569	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13011908	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17220266	0.81[EUR][1000 genomes]
rs2884228	1.00[EUR][1000 genomes]
rs34264824	0.88[EUR][1000 genomes]
rs34412908	0.85[EUR][1000 genomes]
rs34653380	0.88[EUR][1000 genomes]
rs35160861	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36091681	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6722935	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6727015	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71415297	1.00[ASN][1000 genomes]
rs7597542	0.90[ASW][hapmap];0.87[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.87[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][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	nsv533927	chr2:173161637-173796894	Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13005010	ITGA6	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173239200-173260200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:173246200-173260200	Weak transcription	Right Atrium	heart
3	chr2:173249800-173262600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:173250200-173260400	Weak transcription	Thymus	Thymus
5	chr2:173252200-173261400	Weak transcription	Fetal Lung	lung
6	chr2:173253600-173262000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr2:173254400-173261400	Enhancers	Primary hematopoietic stem cells	blood
8	chr2:173254800-173260400	Weak transcription	Left Ventricle	heart
9	chr2:173254800-173261600	Weak transcription	Lung	lung
10	chr2:173255000-173260200	Weak transcription	Fetal Thymus	thymus
11	chr2:173255000-173260200	Weak transcription	Spleen	Spleen
12	chr2:173256000-173262200	Weak transcription	Fetal Intestine Small	intestine
13	chr2:173258000-173259400	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr2:173258200-173259400	Enhancers	Adipose Nuclei	Adipose
15	chr2:173258200-173259400	Enhancers	Skeletal Muscle Female	skeletal muscle
16	chr2:173258200-173261600	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr2:173258400-173259400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr2:173258400-173259400	Enhancers	Fetal Muscle Leg	muscle
19	chr2:173258400-173259400	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr2:173258400-173259600	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr2:173258600-173259400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
22	chr2:173258600-173259400	Enhancers	Aorta	Aorta
23	chr2:173258600-173259400	Enhancers	Fetal Muscle Trunk	muscle
24	chr2:173258600-173259400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
25	chr2:173258800-173260600	Weak transcription	Psoas Muscle	Psoas
26	chr2:173259000-173261000	Weak transcription	Fetal Stomach	stomach
27	chr2:173259000-173268400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr2:173259200-173260400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr2:173259200-173261200	Weak transcription	HSMMtube	muscle
30	chr2:173259200-173261400	Weak transcription	Ovary	ovary
31	chr2:173259200-173262200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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