Variant report

Variant	rs4840488
Chromosome Location	chr8:10368162-10368163
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs12675153	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12675653	0.91[CEU][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12676059	0.91[CEU][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12676436	0.91[CEU][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12677569	0.91[CEU][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12679191	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12681804	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28378036	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28701524	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4269499	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4288337	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4294152	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4333548	0.83[ASN][1000 genomes]
rs4473996	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4480076	0.91[CEU][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4588813	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4623375	0.89[EUR][1000 genomes]
rs4841359	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56246075	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58912510	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs60996714	0.81[EUR][1000 genomes]
rs61094924	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62492775	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62492779	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62492782	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6989332	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6997045	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7009115	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73195174	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7387481	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9657517	0.91[CEU][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030934	chr8:10065169-10561161	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv1022994	chr8:10190618-10660122	Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv539466	chr8:10190618-10660122	Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1025557	chr8:10216726-10555187	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv917085	chr8:10237508-10828204	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv610267	chr8:10268736-10526742	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv1019090	chr8:10303099-10369061	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1024976	chr8:10303099-10385361	Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv1030856	chr8:10303099-10439064	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	nsv610268	chr8:10331636-10486652	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
11	nsv1025251	chr8:10343591-10488557	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
12	nsv1015932	chr8:10357101-10597856	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
13	nsv1026918	chr8:10359634-10390452	Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4840488	PRSS55	cis	parietal	SCAN
rs4840488	XKR6	cis	cerebellum	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:10356400-10368800	Weak transcription	Brain Germinal Matrix	brain
2	chr8:10361000-10368400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr8:10367600-10368200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
4	chr8:10367600-10368200	Active TSS	Duodenum Mucosa	Duodenum
5	chr8:10367600-10368200	Active TSS	Osteobl	bone
6	chr8:10367600-10368400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr8:10367600-10368400	Active TSS	NHDF-Ad	bronchial
8	chr8:10367600-10368400	Active TSS	NHLF	lung
9	chr8:10367600-10368600	Active TSS	Rectal Mucosa Donor 29	rectum
10	chr8:10367600-10368600	Active TSS	Rectal Smooth Muscle	rectum
11	chr8:10367600-10370200	Flanking Active TSS	GM12878-XiMat	blood
12	chr8:10367800-10368200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr8:10367800-10368200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr8:10367800-10368200	Active TSS	Primary T cells fromperipheralblood	blood
15	chr8:10367800-10368200	Active TSS	Primary T helper cells PMA-I stimulated	--
16	chr8:10367800-10368200	Active TSS	Primary T helper cells fromperipheralblood	blood
17	chr8:10367800-10368200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr8:10367800-10368200	Active TSS	Colon Smooth Muscle	Colon
19	chr8:10367800-10368200	Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr8:10367800-10368200	Flanking Active TSS	Fetal Lung	lung
21	chr8:10367800-10368400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr8:10367800-10368400	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
23	chr8:10367800-10368400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
24	chr8:10367800-10370000	Enhancers	Fetal Kidney	kidney
25	chr8:10368000-10368200	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
26	chr8:10368000-10368200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr8:10368000-10369000	Weak transcription	Brain Hippocampus Middle	brain
28	chr8:10368000-10369600	Enhancers	Fetal Stomach	stomach
29	chr8:10368000-10370600	Enhancers	Cortex derived primary cultured neurospheres	brain

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