Variant report

Variant	rs1905139
Chromosome Location	chr2:213393025-213393026
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:213392043..213394903-chr2:213396609..213399566,4	MCF-7	breast:
2	chr2:213392919..213394585-chr2:213396394..213398532,2	K562	blood:

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1026882	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13382807	0.93[ASN][1000 genomes]
rs1351592	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1351594	0.98[ASN][1000 genomes]
rs1384293	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1384294	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1384295	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1531788	0.98[ASN][1000 genomes]
rs1532855	0.85[YRI][hapmap]
rs16848751	0.98[ASN][1000 genomes]
rs1947932	0.98[ASN][1000 genomes]
rs2054617	0.88[CEU][hapmap];0.82[MKK][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes]
rs4233986	0.93[ASN][1000 genomes]
rs4672648	0.85[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs6435707	0.92[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6745293	0.98[ASN][1000 genomes]
rs7556832	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7564590	1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7565622	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7605624	1.00[YRI][hapmap]
rs972491	0.85[CEU][hapmap]
rs979124	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs979125	0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432024	chr2:213314899-213446726	Bivalent/Poised TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv948878	chr2:213345197-213534298	Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1014479	chr2:213370690-213413231	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1905139	FN1	cis	cerebellum	SCAN
rs1905139	LANCL1	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:213384400-213395400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr2:213391600-213399200	Enhancers	Fetal Heart	heart
3	chr2:213392600-213393200	Enhancers	Brain Hippocampus Middle	brain
4	chr2:213392800-213393200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:213392800-213393200	Flanking Active TSS	Aorta	Aorta
6	chr2:213392800-213393200	Flanking Active TSS	Brain Substantia Nigra	brain
7	chr2:213392800-213393200	Enhancers	Right Atrium	heart
8	chr2:213392800-213393200	Active TSS	Right Ventricle	heart
9	chr2:213392800-213393200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
10	chr2:213393000-213393200	Enhancers	Brain Angular Gyrus	brain
11	chr2:213393000-213393200	Enhancers	Brain Cingulate Gyrus	brain
12	chr2:213393000-213393600	Enhancers	Brain Anterior Caudate	brain
13	chr2:213393000-213399000	Weak transcription	Psoas Muscle	Psoas
14	chr2:213393000-213400800	Weak transcription	Skeletal Muscle Male	skeletal muscle

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