Variant report

Variant	rs11772714
Chromosome Location	chr7:50542843-50542844
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	chr7:50540382..50543888-chr7:50545544..50548848,3	K562	blood:

Variant related genes	Relation type
ENSG00000132437	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10239830	0.87[EUR][1000 genomes]
rs10267323	0.89[EUR][1000 genomes]
rs10271341	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[EUR][1000 genomes]
rs10276473	1.00[CEU][hapmap];0.81[CHB][hapmap];0.81[EUR][1000 genomes]
rs10277662	0.89[EUR][1000 genomes]
rs11238133	0.95[JPT][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes]
rs11238134	0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs11575320	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[EUR][1000 genomes]
rs11575463	1.00[CEU][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11761683	0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs12671474	0.89[EUR][1000 genomes]
rs1376524	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17733244	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs1807066	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2060762	0.81[CHB][hapmap];0.86[YRI][hapmap]
rs2060763	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2242042	0.87[EUR][1000 genomes]
rs2329371	1.00[CEU][hapmap];0.81[CHB][hapmap];0.81[EUR][1000 genomes]
rs2876828	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2876829	1.00[CEU][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28889020	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3735273	0.80[CEU][hapmap];0.80[CHB][hapmap];0.81[EUR][1000 genomes]
rs3735275	0.91[YRI][hapmap]
rs3779078	1.00[CEU][hapmap];0.81[CHB][hapmap];0.86[EUR][1000 genomes]
rs3807552	0.81[CHB][hapmap]
rs3807555	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs3807556	1.00[CEU][hapmap];0.81[CHB][hapmap];0.86[EUR][1000 genomes]
rs3807558	1.00[CEU][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6950777	0.81[CHB][hapmap];0.81[EUR][1000 genomes]
rs6963996	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs745042	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs745043	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7776816	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7790758	0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs880029	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs896307	1.00[CEU][hapmap];0.87[YRI][hapmap]
rs896309	1.00[CEU][hapmap];0.85[CHB][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9942686	1.00[CEU][hapmap];0.89[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	nsv1016665	chr7:50452552-51404524	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv888021	chr7:50538589-50610071	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs11772714	FIGNL1	cis	Heart Left Ventricle	GTEx
rs11772714	FIGNL1	cis	Nerve Tibial	GTEx
rs11772714	FIGNL1	cis	Adipose Subcutaneous	GTEx
rs11772714	FIGNL1	cis	Thyroid	GTEx
rs11772714	FIGNL1	cis	multi-tissue	Pritchard
rs11772714	FIGNL1	cis	lung	GTEx
rs11772714	FIGNL1	cis	Artery Tibial	GTEx
rs11772714	FIGNL1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:50535800-50546800	Weak transcription	Pancreas	Pancrea
2	chr7:50535800-50553200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr7:50536200-50545400	Weak transcription	Right Atrium	heart
4	chr7:50536600-50543000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr7:50540800-50543400	Strong transcription	Duodenum Mucosa	Duodenum
6	chr7:50540800-50543400	Enhancers	Skeletal Muscle Male	skeletal muscle
7	chr7:50540800-50543400	Enhancers	Skeletal Muscle Female	skeletal muscle
8	chr7:50541600-50543200	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr7:50541800-50543600	Enhancers	Liver	Liver
10	chr7:50541800-50543800	Weak transcription	Fetal Intestine Large	intestine
11	chr7:50542000-50543000	Enhancers	Adipose Nuclei	Adipose
12	chr7:50542000-50543400	Enhancers	Spleen	Spleen
13	chr7:50542000-50549600	Weak transcription	Stomach Mucosa	stomach
14	chr7:50542200-50543400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr7:50542200-50545000	Weak transcription	HepG2	liver
16	chr7:50542200-50546000	Genic enhancers	Fetal Intestine Small	intestine
17	chr7:50542600-50543000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr7:50542600-50543000	Enhancers	Fetal Muscle Leg	muscle
19	chr7:50542800-50543000	Enhancers	Ovary	ovary
20	chr7:50542800-50543400	Enhancers	Lung	lung
21	chr7:50542800-50544200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr7:50542800-50544200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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