Variant report

Variant	rs1608640
Chromosome Location	chr2:100417041-100417042
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	chr2:100414983..100419771-chr2:100422906..100426417,4	MCF-7	breast:

Extended variants
information (count: 70 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10175788	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10182690	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10191077	0.84[EUR][1000 genomes]
rs10194527	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10198310	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10199548	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10204617	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10496340	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10865032	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10865033	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10865034	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11123796	0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12478013	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12712060	0.90[ASN][1000 genomes]
rs13416974	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13423929	0.80[EUR][1000 genomes]
rs1344701	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1344702	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1346621	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1366761	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1366763	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1366766	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1429268	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1429269	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1568786	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1594111	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1594113	0.82[ASN][1000 genomes]
rs2091150	0.90[EUR][1000 genomes]
rs2115600	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2115601	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2163044	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2309650	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2871310	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4286327	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4481043	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4521099	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4850916	0.84[EUR][1000 genomes]
rs4851231	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4851232	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4851234	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4851235	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62147565	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6542900	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6542901	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6542902	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6542903	0.81[EUR][1000 genomes]
rs6705966	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6721652	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6723474	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6725716	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6732358	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6743473	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6747845	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6756821	0.90[EUR][1000 genomes]
rs7560078	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7562121	0.93[ASN][1000 genomes]
rs7565155	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7566083	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7573572	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7586604	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7596023	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7604536	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9308829	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9967704	0.85[AMR][1000 genomes];1.00[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1608640	IL1RL1	cis	cerebellum	SCAN
rs1608640	C2orf15	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100415400-100418800	Weak transcription	Primary B cells from peripheral blood	blood
2	chr2:100415400-100423400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr2:100416400-100422800	Weak transcription	Primary T cells from cord blood	blood
4	chr2:100417000-100418200	Weak transcription	Primary B cells from cord blood	blood

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