Variant report

Variant	rs11858173
Chromosome Location	chr15:56445730-56445731
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10152826	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10162834	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10163161	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11632218	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11852414	0.82[AMR][1000 genomes]
rs11856691	0.81[AMR][1000 genomes]
rs11858245	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12899534	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12909153	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13379820	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17238601	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17819384	0.86[AFR][1000 genomes]
rs1829543	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2247838	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2460649	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2465405	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2465969	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2584689	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2682027	0.82[AMR][1000 genomes]
rs2682030	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2682031	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2682032	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2682048	0.88[AMR][1000 genomes]
rs2682055	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2713922	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2713934	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2713937	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2713939	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2718905	0.82[AMR][1000 genomes]
rs2718924	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2725871	0.94[ASN][1000 genomes]
rs2947023	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35187662	0.83[AMR][1000 genomes]
rs35840822	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4774238	0.82[AMR][1000 genomes]
rs56274791	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60138831	0.81[AMR][1000 genomes]
rs60648061	0.82[AMR][1000 genomes]
rs62044114	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62047375	0.80[AMR][1000 genomes]
rs62047377	0.80[AMR][1000 genomes]
rs6493836	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6493844	0.82[EUR][1000 genomes]
rs748344	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8032826	0.82[EUR][1000 genomes]
rs8041422	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs894415	0.86[AMR][1000 genomes];0.95[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	nsv833018	chr15:56325799-56492535	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1045906	chr15:56333180-56473614	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56424800-56453800	Weak transcription	Brain Substantia Nigra	brain
2	chr15:56433800-56464000	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr15:56435200-56458800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr15:56435400-56446800	Weak transcription	Primary B cells from peripheral blood	blood
5	chr15:56435400-56447200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr15:56435400-56461000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr15:56435400-56462400	Weak transcription	Fetal Thymus	thymus
8	chr15:56435400-56465200	Weak transcription	Thymus	Thymus
9	chr15:56435800-56454000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr15:56436000-56448600	Weak transcription	K562	blood
11	chr15:56436000-56458000	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr15:56436400-56455800	Weak transcription	Liver	Liver
13	chr15:56436600-56458800	Weak transcription	Primary B cells from cord blood	blood
14	chr15:56441000-56453200	Weak transcription	A549	lung
15	chr15:56441000-56461400	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr15:56442000-56457200	Weak transcription	HMEC	breast
17	chr15:56442000-56458000	Weak transcription	HepG2	liver
18	chr15:56442000-56462600	Weak transcription	HSMM	muscle
19	chr15:56442200-56451000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr15:56442200-56457200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr15:56442600-56470600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr15:56442800-56450800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr15:56442800-56454400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr15:56442800-56462600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr15:56443000-56446000	Weak transcription	Primary T cells from cord blood	blood
26	chr15:56443200-56452200	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr15:56443200-56462600	Weak transcription	Duodenum Mucosa	Duodenum

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