Variant report

Variant	rs1075892
Chromosome Location	chr18:44293214-44293215
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1038005	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11659388	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11663996	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16939988	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17778939	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41471844	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap]
rs4890337	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4890683	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4890685	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56154750	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56350359	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs650329	0.89[TSI][hapmap]
rs9807683	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428355	chr18:44160181-44406285	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv9629	chr18:44264693-44757511	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv909589	chr18:44279892-44330604	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv909590	chr18:44279892-44332911	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv909591	chr18:44279892-44370518	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv909592	chr18:44279892-44385150	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv909593	chr18:44279892-44396246	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
8	nsv909594	chr18:44279892-44400621	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
9	nsv909595	chr18:44279892-44422661	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
10	nsv909596	chr18:44291419-44330604	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv909597	chr18:44291419-44385150	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv909598	chr18:44291419-44422661	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1075892	ST8SIA5	cis	multi-tissue	Pritchard
rs1075892	SIGLEC15	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:44286800-44298800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr18:44287800-44298800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr18:44290000-44293600	Enhancers	Psoas Muscle	Psoas
4	chr18:44290000-44295400	Enhancers	Fetal Muscle Leg	muscle
5	chr18:44290600-44293600	Enhancers	Fetal Muscle Trunk	muscle
6	chr18:44290600-44293600	Enhancers	Left Ventricle	heart
7	chr18:44290600-44294600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr18:44290800-44293800	Enhancers	HSMMtube	muscle
9	chr18:44291000-44293400	Enhancers	NHDF-Ad	bronchial
10	chr18:44291000-44293600	Enhancers	Brain Angular Gyrus	brain
11	chr18:44291200-44293400	Enhancers	HSMM	muscle
12	chr18:44291600-44293400	Enhancers	NH-A	brain
13	chr18:44291600-44293600	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr18:44291800-44295200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr18:44292000-44293800	Enhancers	Fetal Heart	heart
16	chr18:44292000-44294400	Enhancers	Brain Germinal Matrix	brain
17	chr18:44292000-44295000	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr18:44292200-44294400	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr18:44292800-44297000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr18:44293000-44293600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr18:44293000-44294000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr18:44293000-44294000	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr18:44293000-44294400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr18:44293000-44295200	Weak transcription	Right Ventricle	heart
25	chr18:44293000-44296600	Weak transcription	Brain Hippocampus Middle	brain
26	chr18:44293000-44296600	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr18:44293000-44298400	Weak transcription	Ovary	ovary
28	chr18:44293000-44298800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr18:44293200-44293800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr18:44293200-44296600	Weak transcription	Right Atrium	heart
31	chr18:44293200-44296800	Weak transcription	Brain Cingulate Gyrus	brain
32	chr18:44293200-44296800	Weak transcription	Brain Substantia Nigra	brain
33	chr18:44293200-44298400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr18:44293200-44298400	Weak transcription	Osteobl	bone
35	chr18:44293200-44298800	Weak transcription	NHLF	lung

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