Variant report

Variant	rs6945253
Chromosome Location	chr7:50501440-50501441
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10230307	0.83[ASN][1000 genomes]
rs10230343	0.83[ASW][hapmap];0.83[CHB][hapmap];0.86[CHD][hapmap];0.80[GIH][hapmap];0.86[JPT][hapmap];0.89[MEX][hapmap];0.86[YRI][hapmap];0.83[ASN][1000 genomes]
rs10232974	0.83[ASN][1000 genomes]
rs10243511	0.83[ASN][1000 genomes]
rs11768267	0.91[CHD][hapmap];0.80[TSI][hapmap]
rs12719056	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1451376	0.83[ASN][1000 genomes]
rs2060762	0.82[JPT][hapmap]
rs2305358	0.83[ASW][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap];0.86[YRI][hapmap];0.82[ASN][1000 genomes]
rs3735275	0.82[JPT][hapmap]
rs4947510	0.83[CHB][hapmap];0.86[CHD][hapmap];0.80[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.83[ASN][1000 genomes]
rs4947827	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4947954	0.83[ASN][1000 genomes]
rs4947980	0.83[ASN][1000 genomes]
rs732215	0.81[CHD][hapmap]
rs7790230	0.83[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs7803247	0.89[CHD][hapmap]
rs935795	0.81[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	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

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs6945253	FIGNL1	cis	lung	GTEx
rs6945253	FIGNL1	cis	Esophagus Muscularis	GTEx
rs6945253	FIGNL1	cis	cerebellum	SCAN
rs6945253	FIGNL1	cis	Adipose Subcutaneous	GTEx
rs6945253	FIGNL1	cis	Thyroid	GTEx
rs6945253	FIGNL1	cis	Artery Tibial	GTEx
rs6945253	FIGNL1	cis	Nerve Tibial	GTEx
rs6945253	FIGNL1	cis	Skin Sun Exposed Lower leg	GTEx
rs6945253	FIGNL1	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:50486200-50513200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr7:50493400-50505800	Weak transcription	Thymus	Thymus
3	chr7:50495200-50505800	Weak transcription	Fetal Intestine Large	intestine
4	chr7:50495200-50513000	Weak transcription	Duodenum Mucosa	Duodenum
5	chr7:50495200-50517200	Weak transcription	Stomach Mucosa	stomach
6	chr7:50495600-50513800	Weak transcription	HepG2	liver
7	chr7:50496000-50513000	Weak transcription	Gastric	stomach
8	chr7:50496200-50517600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr7:50496800-50505800	Weak transcription	GM12878-XiMat	blood
10	chr7:50498000-50506800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr7:50499400-50506000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr7:50499400-50513000	Weak transcription	Psoas Muscle	Psoas
13	chr7:50499600-50505400	Weak transcription	Fetal Lung	lung
14	chr7:50499800-50506400	Weak transcription	Primary B cells from peripheral blood	blood
15	chr7:50500000-50505600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr7:50500000-50513400	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr7:50500400-50505600	Weak transcription	Primary hematopoietic stem cells	blood
18	chr7:50500600-50513000	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr7:50501000-50517400	Weak transcription	Esophagus	oesophagus

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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