Variant report

Variant	rs4498545
Chromosome Location	chr8:48221724-48221725
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1038797	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs10808752	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs10957074	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11774001	0.92[EUR][1000 genomes]
rs11775514	0.86[EUR][1000 genomes]
rs11775628	0.87[EUR][1000 genomes]
rs11779308	0.92[CEU][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes]
rs11779423	0.89[ASW][hapmap];0.92[CEU][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs11781727	1.00[CEU][hapmap];0.86[CHD][hapmap];0.98[TSI][hapmap];0.90[EUR][1000 genomes]
rs11783141	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11784823	1.00[ASW][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap]
rs11785228	0.93[EUR][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];0.98[TSI][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12543823	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12547513	0.91[EUR][1000 genomes]
rs12680669	0.92[EUR][1000 genomes]
rs12682269	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs13259872	0.89[ASW][hapmap];0.92[CEU][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs13259913	0.89[EUR][1000 genomes]
rs16926260	1.00[YRI][hapmap]
rs2087656	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs2130879	0.86[EUR][1000 genomes]
rs2172121	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs2362554	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[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];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35045730	0.89[EUR][1000 genomes]
rs4242439	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs4388466	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];0.83[JPT][hapmap];0.93[MEX][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs4536257	0.89[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap]
rs4872957	0.92[CEU][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs4873102	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHD][hapmap];0.91[LWK][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs4873106	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]
rs4873293	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4873368	0.82[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs6472229	0.94[EUR][1000 genomes]
rs6981790	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6990123	0.95[EUR][1000 genomes]
rs6994218	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7002441	1.00[YRI][hapmap]
rs7012341	0.91[EUR][1000 genomes]
rs7819806	0.92[CEU][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs7826284	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs7839134	0.92[EUR][1000 genomes]
rs876915	0.82[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
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];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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	nsv530882	chr8:47620846-48223868	ZNF genes & repeats Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS 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
5	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
6	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
7	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
8	nsv916549	chr8:47982642-48223882	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
9	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
10	nsv1023786	chr8:48163412-48235252	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv1031331	chr8:48163412-48239160	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv1032993	chr8:48167423-48246277	Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
13	nsv1030486	chr8:48167423-48247297	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
14	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
15	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
16	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4498545	KIAA0146	cis	parietal	SCAN
rs4498545	MCM4	cis	cerebellum	SCAN

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:48183200-48227800	Weak transcription	Stomach Mucosa	stomach
2	chr8:48189600-48225000	Weak transcription	HUVEC	blood vessel
3	chr8:48199200-48221800	Weak transcription	NHEK	skin
4	chr8:48199200-48227800	Weak transcription	HMEC	breast
5	chr8:48204400-48227800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr8:48204600-48227000	Weak transcription	K562	blood
7	chr8:48204600-48229600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr8:48205000-48227600	Weak transcription	Hela-S3	cervix
9	chr8:48207200-48231200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr8:48207400-48224200	Weak transcription	Spleen	Spleen
11	chr8:48207400-48224600	Weak transcription	HepG2	liver
12	chr8:48207400-48229600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr8:48207400-48238200	Weak transcription	Aorta	Aorta
14	chr8:48207400-48258000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr8:48207600-48227200	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr8:48207600-48245600	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr8:48207600-48248800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr8:48208400-48227800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr8:48208400-48240000	Weak transcription	Placenta	Placenta
20	chr8:48208400-48243800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr8:48208600-48221800	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr8:48208800-48242400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr8:48209000-48227600	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr8:48209400-48227600	Weak transcription	Osteobl	bone
25	chr8:48209400-48230800	Weak transcription	Brain Substantia Nigra	brain
26	chr8:48209400-48266000	Weak transcription	Rectal Smooth Muscle	rectum
27	chr8:48209600-48222000	Weak transcription	Liver	Liver
28	chr8:48209800-48222000	Weak transcription	Brain Hippocampus Middle	brain
29	chr8:48210000-48222200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr8:48210000-48223200	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr8:48210000-48228000	Weak transcription	Left Ventricle	heart
32	chr8:48210000-48242800	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr8:48210600-48222200	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr8:48210600-48243000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr8:48216200-48222400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr8:48216200-48223000	Weak transcription	Fetal Stomach	stomach
37	chr8:48216200-48224200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr8:48216200-48224200	Weak transcription	Esophagus	oesophagus
39	chr8:48216200-48227800	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr8:48216200-48228400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr8:48216200-48228600	Weak transcription	Lung	lung
42	chr8:48216200-48229600	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr8:48216200-48229600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr8:48216200-48229600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr8:48216200-48229600	Weak transcription	Pancreas	Pancrea
46	chr8:48216200-48229800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr8:48216200-48249600	Weak transcription	Ovary	ovary
48	chr8:48216200-48252400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr8:48216400-48232200	Weak transcription	Thymus	Thymus
50	chr8:48216600-48229600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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