Variant report

Variant	rs888953
Chromosome Location	chr5:148120039-148120040
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	chr5:148118964..148121513-chr5:148480398..148481961,2	MCF-7	breast:
2	chr5:148115590..148117219-chr5:148117316..148121012,3	K562	blood:

Extended variants
information (count: 97 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10078593	0.80[EUR][1000 genomes]
rs10078616	0.89[EUR][1000 genomes]
rs10747517	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10747518	0.90[EUR][1000 genomes]
rs10875640	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11168059	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11168060	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11168061	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11168062	0.89[EUR][1000 genomes]
rs11747905	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11750926	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12189260	0.89[EUR][1000 genomes]
rs12517142	0.90[EUR][1000 genomes]
rs12653443	0.90[EUR][1000 genomes]
rs12654719	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1368279	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17108721	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs185021	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2082397	0.90[EUR][1000 genomes]
rs2082398	0.90[EUR][1000 genomes]
rs2163751	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2163752	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2400644	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2400645	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2400702	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2400703	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2400704	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs246502	0.85[EUR][1000 genomes]
rs246504	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2568940	0.88[EUR][1000 genomes]
rs2569000	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2569001	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2895774	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs30305	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs30306	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs30307	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs30308	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs30309	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs30310	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs30311	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs30312	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs30313	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs30314	0.88[EUR][1000 genomes]
rs30315	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs30316	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs30317	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs30318	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs30320	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs30321	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs30322	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs30323	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs30324	0.87[EUR][1000 genomes]
rs30325	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs30326	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs30327	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs30328	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs30329	0.87[EUR][1000 genomes]
rs30330	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs30331	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3097815	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs39835	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs40949	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4513680	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4705058	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4705261	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4705262	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4705263	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4705265	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56043944	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56376672	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59386367	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59598688	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62388002	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6580579	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6580580	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6861953	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6865781	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6867058	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6870415	0.90[EUR][1000 genomes]
rs6870429	0.90[EUR][1000 genomes]
rs6870766	0.90[EUR][1000 genomes]
rs6874249	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6874997	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6879964	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6882470	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6882476	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6883606	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6885216	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6886359	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6892967	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7702609	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7737439	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs888954	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs888955	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs919723	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs919724	0.90[EUR][1000 genomes];0.83[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	nsv883021	chr5:148060817-148182123	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs888953	ZNF300	cis	parietal	SCAN
rs888953	PLAC8L1	cis	parietal	SCAN
rs888953	SPINK14	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:148111400-148120400	Weak transcription	Duodenum Mucosa	Duodenum
2	chr5:148113600-148120400	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr5:148114000-148120800	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr5:148115200-148121400	Enhancers	Adipose Nuclei	Adipose
5	chr5:148115400-148120400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr5:148115600-148121000	Weak transcription	HUVEC	blood vessel
7	chr5:148116600-148120800	Weak transcription	Brain Substantia Nigra	brain
8	chr5:148117200-148120600	Weak transcription	Psoas Muscle	Psoas
9	chr5:148118200-148121000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr5:148118800-148121400	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr5:148119000-148120400	Enhancers	Skeletal Muscle Male	skeletal muscle
12	chr5:148119000-148121000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr5:148119000-148121000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
14	chr5:148119000-148121200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr5:148119200-148120800	Enhancers	Placenta	Placenta
16	chr5:148119200-148121400	Enhancers	Fetal Heart	heart
17	chr5:148119200-148121600	Enhancers	Liver	Liver
18	chr5:148119600-148120600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr5:148119600-148120600	Weak transcription	HepG2	liver
20	chr5:148119600-148120800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr5:148119600-148120800	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr5:148119600-148121000	Enhancers	NHLF	lung
23	chr5:148119600-148121600	Enhancers	Colon Smooth Muscle	Colon
24	chr5:148119600-148121600	Enhancers	Fetal Stomach	stomach
25	chr5:148119600-148126200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr5:148119600-148126200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr5:148119600-148126400	Weak transcription	Fetal Lung	lung
28	chr5:148119600-148135000	Weak transcription	Right Atrium	heart
29	chr5:148119800-148120800	Enhancers	Primary B cells from cord blood	blood
30	chr5:148119800-148120800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr5:148119800-148120800	Enhancers	HSMMtube	muscle
32	chr5:148120000-148121000	Enhancers	Rectal Mucosa Donor 31	rectum

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