Variant report

Variant	rs2488540
Chromosome Location	chr6:37488116-37488117
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:37486519..37488969-chr6:37490130..37493160,3	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10807184	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10947675	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11969056	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12202055	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12202664	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1757169	0.80[ASN][1000 genomes]
rs1757171	0.80[ASN][1000 genomes]
rs1757173	0.80[ASN][1000 genomes]
rs1757180	0.80[ASN][1000 genomes]
rs1757186	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1757188	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1757189	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1757191	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1776454	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1776455	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2776870	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2776872	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2776874	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2776875	0.80[ASN][1000 genomes]
rs2776877	0.80[ASN][1000 genomes]
rs2776878	0.81[ASN][1000 genomes]
rs2776920	0.81[EUR][1000 genomes]
rs2797795	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2797796	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2797798	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2797799	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2797801	0.80[ASN][1000 genomes]
rs2797803	0.81[ASN][1000 genomes]
rs3818985	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3818986	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62408395	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6903910	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6921922	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs882322	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs914348	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9349039	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9366935	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9369005	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9380677	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752124	chr6:37416219-37680622	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
2	nsv1016310	chr6:37473075-37528469	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2488540	RP1-153P14.5	cis	lung	GTEx
rs2488540	RP1-153P14.5	cis	Whole Blood	GTEx
rs2488540	RP1-153P14.8	cis	Whole Blood	GTEx

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37486400-37488400	Weak transcription	Dnd41	blood
2	chr6:37486400-37488600	Weak transcription	Primary hematopoietic stem cells	blood
3	chr6:37486400-37488600	Weak transcription	Fetal Brain Female	brain
4	chr6:37486400-37488800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr6:37486400-37490400	Enhancers	Primary T cells fromperipheralblood	blood
6	chr6:37486400-37490800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
7	chr6:37486600-37489800	Enhancers	Fetal Thymus	thymus
8	chr6:37486800-37488600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr6:37486800-37488600	Weak transcription	Fetal Brain Male	brain
10	chr6:37486800-37491400	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr6:37487200-37488400	Weak transcription	Thymus	Thymus
12	chr6:37487400-37488400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr6:37487400-37488400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr6:37487400-37490800	Weak transcription	Right Atrium	heart
15	chr6:37487400-37491000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr6:37487400-37492400	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr6:37487600-37488200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr6:37487600-37488400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr6:37487600-37488400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr6:37487600-37488600	Weak transcription	Primary T cells from cord blood	blood
21	chr6:37487600-37488600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr6:37487600-37498200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr6:37487800-37488200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr6:37487800-37488200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr6:37487800-37488400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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