Variant report

Variant	rs4873269
Chromosome Location	chr8:48251764-48251765
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10099236	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10108778	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10441557	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10957370	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11776864	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12547497	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13279327	0.90[CHD][hapmap];0.80[GIH][hapmap];0.93[JPT][hapmap]
rs2362555	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34506397	0.93[ASN][1000 genomes]
rs35332377	1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4873101	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4873463	0.93[JPT][hapmap]
rs58299877	0.88[EUR][1000 genomes]
rs6472452	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs6473996	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6981485	0.92[EUR][1000 genomes]
rs6987882	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6990363	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];0.80[JPT][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs7825148	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7828350	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7831310	0.81[EUR][1000 genomes]
rs7832841	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7833589	0.90[CHD][hapmap];0.89[GIH][hapmap];0.93[JPT][hapmap]
rs7835668	0.87[ASN][1000 genomes]
rs7846620	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028036	chr8:47531749-48256108	Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	nsv1019289	chr8:47536056-48251883	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
3	nsv539591	chr8:47536056-48251883	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	nsv1015347	chr8:47698082-48318579	Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
5	nsv539593	chr8:47698082-48318579	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
6	esv3693377	chr8:47824261-48582964	Genic enhancers Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
7	nsv491863	chr8:48053825-48586176	Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	esv2758155	chr8:48188989-48321308	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	esv2759610	chr8:48188989-48321308	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	esv1817304	chr8:48205314-48321308	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4873269	KIAA0146	cis	parietal	SCAN
rs4873269	MCM4	cis	lymphoblastoid	seeQTL
rs4873269	SNAI2	cis	cerebellum	SCAN
rs4873269	MCM4	cis	cerebellum	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:48207400-48258000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr8:48209400-48266000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr8:48216200-48252400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr8:48223400-48252600	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr8:48228200-48254400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr8:48228200-48256000	Weak transcription	Left Ventricle	heart
7	chr8:48228600-48265800	Weak transcription	K562	blood
8	chr8:48230000-48252400	Weak transcription	Lung	lung
9	chr8:48230400-48252200	Weak transcription	Fetal Stomach	stomach
10	chr8:48230400-48256200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr8:48230400-48267400	Weak transcription	Spleen	Spleen
12	chr8:48230600-48252800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr8:48236400-48252800	Weak transcription	Pancreas	Pancrea
14	chr8:48237600-48256000	Weak transcription	Esophagus	oesophagus
15	chr8:48238800-48274600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr8:48239000-48255200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr8:48239000-48265800	Weak transcription	Aorta	Aorta
18	chr8:48239600-48254200	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr8:48240600-48253400	Weak transcription	Placenta	Placenta
20	chr8:48244200-48255800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr8:48244200-48255800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr8:48244200-48256000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr8:48244200-48256000	Weak transcription	Fetal Lung	lung
24	chr8:48244200-48256200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr8:48245800-48254400	Weak transcription	Brain Cingulate Gyrus	brain
26	chr8:48247800-48276400	Weak transcription	Colonic Mucosa	Colon
27	chr8:48248800-48309600	Weak transcription	Thymus	Thymus
28	chr8:48249200-48252200	Weak transcription	Primary T cells from cord blood	blood
29	chr8:48249200-48253000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr8:48249200-48253800	Weak transcription	Fetal Intestine Small	intestine
31	chr8:48249200-48254200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr8:48249200-48256000	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr8:48249200-48256000	Weak transcription	NHEK	skin
34	chr8:48249200-48265600	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr8:48249200-48282000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr8:48249400-48254800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr8:48249600-48252400	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr8:48249600-48252800	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr8:48249600-48252800	Weak transcription	A549	lung
40	chr8:48249600-48255800	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr8:48249600-48256000	Weak transcription	Primary B cells from peripheral blood	blood
42	chr8:48249800-48252800	Weak transcription	Dnd41	blood
43	chr8:48249800-48254400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr8:48249800-48266000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr8:48249800-48267200	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr8:48249800-48277400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr8:48249800-48277800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr8:48250000-48252600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr8:48250000-48254200	Weak transcription	Primary B cells from cord blood	blood
50	chr8:48250000-48254400	Weak transcription	Ovary	ovary

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