Variant report

Variant	rs4292660
Chromosome Location	chr8:99796296-99796297
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10447977	0.83[CHD][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap]
rs10755896	0.82[MEX][hapmap]
rs10755897	0.83[MEX][hapmap];0.84[TSI][hapmap]
rs11774463	0.83[MEX][hapmap]
rs11778767	0.93[GIH][hapmap];0.81[TSI][hapmap]
rs11780500	0.93[GIH][hapmap];0.84[TSI][hapmap]
rs11785245	0.81[AMR][1000 genomes]
rs12114834	0.83[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.81[TSI][hapmap]
rs12547297	0.83[MEX][hapmap];0.84[TSI][hapmap]
rs12549803	0.84[TSI][hapmap]
rs12550783	0.83[MEX][hapmap];0.84[TSI][hapmap]
rs12679734	0.83[CHD][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap]
rs12680195	0.83[MEX][hapmap];0.82[TSI][hapmap]
rs13269932	0.89[GIH][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap]
rs13275915	0.89[GIH][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap]
rs1447245	0.91[JPT][hapmap]
rs1476181	1.00[JPT][hapmap]
rs2442012	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2442014	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2515214	0.83[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2515216	0.92[GIH][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs2515219	0.80[EUR][1000 genomes]
rs2922066	0.91[JPT][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap]
rs2922076	0.91[JPT][hapmap]
rs2922078	0.89[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap]
rs2922082	0.81[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap]
rs34366206	0.83[CHD][hapmap];0.82[JPT][hapmap]
rs35798019	0.82[ASW][hapmap];0.93[GIH][hapmap];0.88[TSI][hapmap];0.96[YRI][hapmap]
rs4131873	0.83[GIH][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap]
rs4255105	0.83[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap]
rs4279561	0.87[MEX][hapmap];0.84[TSI][hapmap]
rs4304299	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4413739	1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4549741	0.83[GIH][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap]
rs4562286	0.83[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes]
rs4734410	0.89[GIH][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap]
rs4734414	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4735568	0.84[TSI][hapmap]
rs4735574	0.89[GIH][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap]
rs58679407	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs58993030	0.80[EUR][1000 genomes]
rs62532587	0.81[AMR][1000 genomes]
rs6988087	0.80[CEU][hapmap];0.80[CHB][hapmap];0.96[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6992925	0.89[GIH][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap]
rs7818828	0.80[CHB][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes]
rs7827435	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7845271	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9656842	0.84[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv891218	chr8:99507313-99906221	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv1027025	chr8:99672977-100115315	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv539690	chr8:99672977-100115315	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv891220	chr8:99681858-99867419	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
5	nsv1025685	chr8:99706280-99826236	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv539691	chr8:99706280-99826236	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	nsv1031089	chr8:99715785-100399935	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
8	nsv981968	chr8:99794499-99809509	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4292660	NCALD	cis	cerebellum	SCAN
rs4292660	OSR2	cis	cerebellum	SCAN
rs4292660	RGS22	cis	cerebellum	SCAN
rs4292660	STK3	cis	parietal	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:99776600-99798600	Weak transcription	Fetal Heart	heart
2	chr8:99776800-99797800	Weak transcription	Stomach Smooth Muscle	stomach
3	chr8:99779000-99796400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr8:99779000-99796400	Weak transcription	Aorta	Aorta
5	chr8:99779000-99796400	Weak transcription	Fetal Lung	lung
6	chr8:99785000-99796600	Weak transcription	Fetal Muscle Trunk	muscle
7	chr8:99792800-99796400	Enhancers	Liver	Liver
8	chr8:99793000-99796400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr8:99793800-99796600	Weak transcription	Colon Smooth Muscle	Colon
10	chr8:99794000-99796400	Weak transcription	HSMMtube	muscle
11	chr8:99794600-99796400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr8:99794600-99796400	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr8:99794600-99796600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr8:99794800-99796400	Weak transcription	Primary T cells from cord blood	blood
15	chr8:99794800-99796400	Weak transcription	Fetal Thymus	thymus
16	chr8:99794800-99796400	Weak transcription	Gastric	stomach
17	chr8:99794800-99796400	Weak transcription	Pancreas	Pancrea
18	chr8:99794800-99796400	Weak transcription	Right Ventricle	heart
19	chr8:99794800-99796400	Weak transcription	Thymus	Thymus
20	chr8:99795000-99796400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr8:99795600-99796400	Weak transcription	K562	blood
22	chr8:99795600-99797400	ZNF genes & repeats	GM12878-XiMat	blood
23	chr8:99795800-99797000	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
24	chr8:99795800-99798600	ZNF genes & repeats	A549	lung
25	chr8:99796000-99796400	Enhancers	Ovary	ovary
26	chr8:99796000-99796400	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr8:99796000-99797000	Enhancers	Brain Angular Gyrus	brain
28	chr8:99796000-99797400	ZNF genes & repeats	Fetal Muscle Leg	muscle
29	chr8:99796000-99798800	ZNF genes & repeats	Fetal Intestine Small	intestine
30	chr8:99796200-99796400	Flanking Active TSS	Adipose Nuclei	Adipose
31	chr8:99796200-99796400	Weak transcription	Stomach Mucosa	stomach
32	chr8:99796200-99796600	Enhancers	Brain Substantia Nigra	brain
33	chr8:99796200-99796600	Enhancers	NHDF-Ad	bronchial
34	chr8:99796200-99796800	Enhancers	Brain Hippocampus Middle	brain
35	chr8:99796200-99796800	Enhancers	Left Ventricle	heart
36	chr8:99796200-99797000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
37	chr8:99796200-99797000	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
38	chr8:99796200-99797200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr8:99796200-99797200	Enhancers	Psoas Muscle	Psoas
40	chr8:99796200-99797400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
41	chr8:99796200-99797400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr8:99796200-99797800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
43	chr8:99796200-99797800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr8:99796200-99797800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
45	chr8:99796200-99797800	ZNF genes & repeats	Osteobl	bone
46	chr8:99796200-99798000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr8:99796200-99798000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
48	chr8:99796200-99798000	ZNF genes & repeats	Fetal Intestine Large	intestine
49	chr8:99796200-99798000	ZNF genes & repeats	Placenta	Placenta
50	chr8:99796200-99798000	ZNF genes & repeats	Fetal Stomach	stomach

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