Variant report

Variant	rs4873106
Chromosome Location	chr8:48362889-48362890
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1038797	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs10808752	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs10957074	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11774001	0.97[EUR][1000 genomes]
rs11775514	0.91[EUR][1000 genomes]
rs11775628	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11779423	0.80[EUR][1000 genomes]
rs11781727	1.00[CEU][hapmap];0.86[CHD][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs11783141	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11784823	1.00[ASW][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs11785228	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12541086	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs12543823	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12547513	0.98[EUR][1000 genomes]
rs12680669	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12682269	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs13259872	0.81[EUR][1000 genomes]
rs13259913	0.99[EUR][1000 genomes]
rs16926260	1.00[YRI][hapmap]
rs2087656	1.00[CEU][hapmap];0.87[CHD][hapmap];0.98[TSI][hapmap];0.94[EUR][1000 genomes]
rs2130413	1.00[ASW][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap]
rs2130879	0.93[EUR][1000 genomes]
rs2171854	1.00[YRI][hapmap]
rs2172121	1.00[CEU][hapmap];0.87[CHD][hapmap];0.98[TSI][hapmap];0.97[EUR][1000 genomes]
rs2362554	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34099416	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35045730	0.97[EUR][1000 genomes]
rs35235599	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4242439	0.80[EUR][1000 genomes]
rs4388466	0.81[EUR][1000 genomes]
rs4498545	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.91[EUR][1000 genomes]
rs4536257	0.89[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs4872957	0.81[EUR][1000 genomes]
rs4873102	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHD][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.98[EUR][1000 genomes]
rs4873292	0.84[ASN][1000 genomes]
rs4873293	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4873368	0.82[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs4873395	1.00[ASW][hapmap];0.81[MKK][hapmap]
rs4873477	1.00[YRI][hapmap]
rs6472229	0.90[EUR][1000 genomes]
rs6981790	0.93[EUR][1000 genomes]
rs6990123	0.93[EUR][1000 genomes]
rs6994218	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7002441	1.00[YRI][hapmap]
rs7012341	0.98[EUR][1000 genomes]
rs7819806	0.81[EUR][1000 genomes]
rs7826284	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs7839134	0.91[EUR][1000 genomes]
rs876915	0.82[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs902619	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv1034660	chr8:48265109-48411279	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1025674	chr8:48306843-48548862	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1023409	chr8:48320442-48454089	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv539595	chr8:48320442-48454089	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4873106	MCM4	cis	cerebellum	SCAN
rs4873106	KIAA0146	cis	parietal	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:48312800-48367600	Weak transcription	Pancreas	Pancrea
2	chr8:48312800-48377000	Weak transcription	Esophagus	oesophagus
3	chr8:48323000-48364400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr8:48326000-48366000	Weak transcription	Gastric	stomach
5	chr8:48328600-48364000	Weak transcription	Fetal Intestine Large	intestine
6	chr8:48328600-48371400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr8:48328600-48374600	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr8:48335400-48363400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr8:48340400-48364000	Weak transcription	Lung	lung
10	chr8:48340600-48365600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr8:48342200-48372600	Weak transcription	Liver	Liver
12	chr8:48342600-48364000	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr8:48343800-48366800	Weak transcription	Aorta	Aorta
14	chr8:48343800-48371400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr8:48344200-48363200	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr8:48344400-48363200	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr8:48345000-48369800	Weak transcription	NH-A	brain
18	chr8:48345000-48370600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr8:48347200-48366000	Weak transcription	Fetal Thymus	thymus
20	chr8:48349600-48363800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr8:48349600-48363800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr8:48351000-48363800	Weak transcription	Fetal Stomach	stomach
23	chr8:48351400-48387000	Weak transcription	Left Ventricle	heart
24	chr8:48351600-48364200	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr8:48352400-48364000	Weak transcription	Adipose Nuclei	Adipose
26	chr8:48352400-48365200	Weak transcription	Brain Anterior Caudate	brain
27	chr8:48353000-48374400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr8:48353000-48390600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr8:48353200-48364000	Weak transcription	Fetal Muscle Trunk	muscle
30	chr8:48353200-48364000	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr8:48353400-48364200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr8:48353400-48364400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr8:48353400-48374600	Weak transcription	Fetal Kidney	kidney
34	chr8:48353400-48374600	Weak transcription	HSMMtube	muscle
35	chr8:48353400-48382000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr8:48353600-48363400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr8:48353600-48363800	Weak transcription	Fetal Lung	lung
38	chr8:48353600-48364200	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr8:48353800-48363000	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr8:48354000-48365200	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr8:48357400-48363800	Weak transcription	HSMM	muscle
42	chr8:48357400-48370400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr8:48358000-48364800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
44	chr8:48358400-48374600	Weak transcription	Psoas Muscle	Psoas
45	chr8:48358800-48371400	Weak transcription	Dnd41	blood
46	chr8:48359000-48364000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr8:48359000-48371200	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr8:48361000-48363000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr8:48361200-48364800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr8:48361400-48363000	ZNF genes & repeats	Primary B cells from cord blood	blood

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