Variant report

Variant	rs7597542
Chromosome Location	chr2:173267613-173267614
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	chr2:173266015..173268775-chr2:173291252..173293915,2	MCF-7	breast:
2	chr2:173265324..173267931-chr2:173283487..173286402,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000226963	Chromatin interaction
ENSG00000091409	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12996569	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs13005010	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs13011908	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17220266	0.96[EUR][1000 genomes]
rs35160861	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs36091681	0.95[AMR][1000 genomes]
rs6722935	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6727015	0.84[AMR][1000 genomes];0.95[EUR][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	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
2	nsv875414	chr2:173267081-173307756	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7597542	ITGA6	cis	parietal	SCAN
rs7597542	GAD1	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173259000-173268400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr2:173262200-173269600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr2:173262600-173268000	Weak transcription	Esophagus	oesophagus
4	chr2:173263400-173268000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr2:173263400-173268200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr2:173263400-173273000	Weak transcription	Right Atrium	heart
7	chr2:173263600-173272800	Weak transcription	Fetal Muscle Leg	muscle
8	chr2:173264600-173268000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr2:173264600-173268200	Weak transcription	Lung	lung
10	chr2:173264800-173268000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr2:173266800-173268600	Enhancers	Left Ventricle	heart
12	chr2:173266800-173268600	Enhancers	Right Ventricle	heart
13	chr2:173266800-173268800	Enhancers	Adipose Nuclei	Adipose
14	chr2:173267200-173268200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr2:173267200-173268200	Weak transcription	HUVEC	blood vessel
16	chr2:173267400-173268400	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr2:173267400-173268400	Enhancers	NHEK	skin
18	chr2:173267400-173268600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr2:173267600-173268000	Weak transcription	Fetal Thymus	thymus
20	chr2:173267600-173270600	Enhancers	HMEC	breast
21	chr2:173267600-173275600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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