Variant report

Variant	rs7554154
Chromosome Location	chr1:92933558-92933559
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RPAP2-3	chr1:92933167-92933655	NONHSAT004458

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10874637	0.88[ASN][1000 genomes]
rs10875349	0.92[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs11164288	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs11164349	0.86[EUR][1000 genomes]
rs11164546	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11578098	1.00[JPT][hapmap]
rs11581176	1.00[JPT][hapmap]
rs11589122	1.00[JPT][hapmap]
rs11800771	1.00[JPT][hapmap]
rs11800848	1.00[JPT][hapmap]
rs11803383	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11803457	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs11804321	1.00[JPT][hapmap]
rs11805007	1.00[JPT][hapmap]
rs11808092	1.00[JPT][hapmap]
rs12024731	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12086394	0.84[EUR][1000 genomes]
rs12743520	1.00[JPT][hapmap]
rs12756786	1.00[JPT][hapmap]
rs1325435	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1415296	1.00[JPT][hapmap]
rs1487536	0.96[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs1487540	0.96[CEU][hapmap];1.00[CHB][hapmap]
rs1542685	0.96[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs2087194	0.96[CEU][hapmap];1.00[CHB][hapmap]
rs2391161	0.82[EUR][1000 genomes]
rs3103178	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs3103181	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs3131813	0.83[EUR][1000 genomes]
rs3131814	0.96[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs3790450	1.00[JPT][hapmap]
rs3929737	0.86[EUR][1000 genomes]
rs4393167	0.86[EUR][1000 genomes]
rs4414050	0.90[EUR][1000 genomes]
rs4642892	1.00[JPT][hapmap]
rs4658300	0.96[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs58394161	0.88[ASN][1000 genomes]
rs6603962	0.96[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs6603971	0.86[EUR][1000 genomes]
rs6603973	0.88[ASN][1000 genomes]
rs6603974	0.88[ASN][1000 genomes]
rs6604090	0.96[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs6661384	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs6663114	0.84[EUR][1000 genomes]
rs6663118	0.83[EUR][1000 genomes]
rs6663278	0.96[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs6668803	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs6692287	0.83[EUR][1000 genomes]
rs6702267	0.96[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs733012	0.87[EUR][1000 genomes]
rs745793	0.86[EUR][1000 genomes]
rs7517541	0.93[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs7518974	0.85[EUR][1000 genomes]
rs7520275	0.96[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs7539757	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7543947	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs912794	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9440085	0.82[EUR][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	nsv523354	chr1:92931263-93064823	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:92925600-92946000	Weak transcription	Right Atrium	heart
2	chr1:92926200-92934200	Enhancers	Dnd41	blood
3	chr1:92926400-92933600	Enhancers	Primary neutrophils fromperipheralblood	blood
4	chr1:92929400-92940600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr1:92929600-92933600	Enhancers	Primary hematopoietic stem cells	blood
6	chr1:92929600-92940800	Weak transcription	Duodenum Mucosa	Duodenum
7	chr1:92930600-92939000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr1:92930600-92939400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr1:92930800-92944400	Weak transcription	Spleen	Spleen
10	chr1:92931000-92939000	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr1:92931000-92939000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr1:92931400-92935000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr1:92931800-92933600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr1:92932600-92933600	Enhancers	Fetal Thymus	thymus
15	chr1:92933000-92939600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr1:92933000-92939800	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr1:92933200-92938200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr1:92933400-92938600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr1:92933400-92939000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr1:92933400-92939000	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr1:92933400-92939000	Weak transcription	Thymus	Thymus
22	chr1:92933400-92941200	Weak transcription	Primary T cells from cord blood	blood

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