Variant report

Variant	rs2115600
Chromosome Location	chr2:100397631-100397632
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	chr2:100392836..100396080-chr2:100396226..100398545,3	MCF-7	breast:
2	chr2:100396107..100398536-chr2:100399998..100402177,2	K562	blood:

Extended variants
information (count: 75 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10191816	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10194527	0.86[ASN][1000 genomes]
rs10198310	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10199548	0.91[ASN][1000 genomes]
rs10199818	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10204617	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10496340	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10865032	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11123793	0.86[EUR][1000 genomes]
rs11123794	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11123795	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11123796	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11682978	0.87[EUR][1000 genomes]
rs11690403	0.85[EUR][1000 genomes]
rs11888741	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12712059	0.87[EUR][1000 genomes]
rs12712060	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs13010551	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1344701	0.85[ASN][1000 genomes]
rs1344702	0.86[ASN][1000 genomes]
rs1366761	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1366763	0.82[ASN][1000 genomes]
rs1366766	0.86[ASN][1000 genomes]
rs1404175	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1404177	0.87[EUR][1000 genomes]
rs1429268	0.85[ASN][1000 genomes]
rs1429269	0.85[ASN][1000 genomes]
rs1568786	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1594111	0.82[ASN][1000 genomes]
rs1594113	0.82[ASN][1000 genomes]
rs1608640	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2030690	0.81[EUR][1000 genomes]
rs2309650	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2309690	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2871310	0.82[ASN][1000 genomes]
rs3863005	0.87[EUR][1000 genomes]
rs3915083	0.87[EUR][1000 genomes]
rs4286327	0.82[ASN][1000 genomes]
rs4481043	0.86[ASN][1000 genomes]
rs4521099	0.84[ASN][1000 genomes]
rs4850914	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4851225	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4851226	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4851228	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4851230	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4851231	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4851235	0.85[ASN][1000 genomes]
rs62147565	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6542891	0.82[EUR][1000 genomes]
rs6542900	0.84[ASN][1000 genomes]
rs6542901	0.85[ASN][1000 genomes]
rs6723474	0.86[ASN][1000 genomes]
rs6725716	0.87[ASN][1000 genomes]
rs6739478	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6739601	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6741990	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6756009	0.82[EUR][1000 genomes]
rs6757262	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6758027	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7559975	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7560078	0.87[ASN][1000 genomes]
rs7562121	0.95[AFR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7566083	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7582469	0.87[EUR][1000 genomes]
rs7584365	0.87[EUR][1000 genomes]
rs7589376	0.82[EUR][1000 genomes]
rs7596023	0.87[ASN][1000 genomes]
rs7602699	0.80[EUR][1000 genomes]
rs9967704	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431424	chr2:99652682-100494682	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv1003343	chr2:100241560-100848900	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv535843	chr2:100241560-100848900	Genic enhancers Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	esv2757820	chr2:100380891-100546675	Enhancers Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	esv2759078	chr2:100380891-100546675	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv1010971	chr2:100387986-100431935	Weak transcription ZNF genes & repeats Strong transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2115600	NFXL1	trans	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100384200-100404400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr2:100389600-100399400	Weak transcription	Ovary	ovary
3	chr2:100389600-100400800	Weak transcription	Placenta	Placenta
4	chr2:100393800-100404000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr2:100394000-100403000	Weak transcription	Fetal Brain Female	brain
6	chr2:100394400-100405800	Weak transcription	Lung	lung
7	chr2:100394600-100400400	Weak transcription	Thymus	Thymus
8	chr2:100395000-100403600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr2:100395600-100397800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
10	chr2:100395600-100402400	Weak transcription	Fetal Brain Male	brain
11	chr2:100395800-100399000	Weak transcription	Fetal Lung	lung
12	chr2:100396200-100400600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr2:100396200-100407600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr2:100396200-100409200	Strong transcription	Primary B cells from cord blood	blood
15	chr2:100397400-100399000	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr2:100397400-100399600	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr2:100397400-100399600	Weak transcription	Primary T cells from cord blood	blood
18	chr2:100397400-100409800	Strong transcription	Primary B cells from peripheral blood	blood

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