Variant report

Variant	rs478259
Chromosome Location	chr3:105283024-105283025
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs12630003	0.81[AFR][1000 genomes]
rs17189452	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3772551	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.82[LWK][hapmap];0.90[MKK][hapmap];0.84[TSI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3772554	0.90[ASW][hapmap];1.00[CEU][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.87[TSI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs485922	0.90[ASW][hapmap];1.00[CEU][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.87[TSI][hapmap];0.93[YRI][hapmap];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4894832	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs490029	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs519016	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.83[LWK][hapmap];0.91[MKK][hapmap];0.87[TSI][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs526375	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs526963	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs562960	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs577295	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs610047	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs620165	0.92[ASN][1000 genomes]
rs629187	0.90[ASW][hapmap];1.00[CEU][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.87[TSI][hapmap];0.93[YRI][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs66875175	0.85[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525071	chr3:105004853-105409321	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv534224	chr3:105141696-105404293	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
3	nsv829651	chr3:105203424-105402136	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv460811	chr3:105212993-105316769	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
5	nsv591240	chr3:105212993-105316769	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs478259	ALCAM	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105221400-105300400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:105242000-105293600	Weak transcription	Lung	lung
3	chr3:105246600-105284400	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr3:105248400-105291200	Weak transcription	Brain Cingulate Gyrus	brain
5	chr3:105249800-105284000	Weak transcription	Fetal Stomach	stomach
6	chr3:105249800-105285200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr3:105260800-105297000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr3:105260800-105299800	Weak transcription	Pancreas	Pancrea
9	chr3:105263000-105295400	Weak transcription	Brain Angular Gyrus	brain
10	chr3:105267600-105293800	Weak transcription	Brain Anterior Caudate	brain
11	chr3:105268400-105297800	Weak transcription	NHLF	lung
12	chr3:105271600-105297000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr3:105271600-105303000	Weak transcription	Aorta	Aorta
14	chr3:105271800-105285800	Weak transcription	HUVEC	blood vessel
15	chr3:105272000-105291200	Weak transcription	Brain Substantia Nigra	brain
16	chr3:105272200-105312800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr3:105272400-105302800	Weak transcription	NHEK	skin
18	chr3:105273000-105295200	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr3:105273200-105292200	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr3:105273200-105294000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr3:105273200-105295800	Weak transcription	Duodenum Mucosa	Duodenum
22	chr3:105273200-105303000	Weak transcription	HMEC	breast
23	chr3:105273400-105285600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr3:105273400-105287800	Weak transcription	Primary B cells from peripheral blood	blood
25	chr3:105273400-105292800	Weak transcription	Ovary	ovary
26	chr3:105273400-105297600	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr3:105273400-105297600	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr3:105273400-105299800	Weak transcription	NHDF-Ad	bronchial
29	chr3:105273600-105283200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr3:105273800-105291000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr3:105273800-105297400	Weak transcription	Primary hematopoietic stem cells	blood
32	chr3:105274000-105291200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr3:105274000-105303000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr3:105274600-105293400	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr3:105277200-105299200	Weak transcription	Brain Hippocampus Middle	brain
36	chr3:105277400-105284400	Weak transcription	NH-A	brain
37	chr3:105278600-105287200	Weak transcription	HSMM	muscle
38	chr3:105278600-105289800	Weak transcription	Primary B cells from cord blood	blood
39	chr3:105278600-105290800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr3:105278600-105297000	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr3:105278600-105297400	Weak transcription	GM12878-XiMat	blood
42	chr3:105278800-105289200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr3:105278800-105290600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr3:105278800-105290800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr3:105279200-105283400	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr3:105280800-105283200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr3:105281200-105283200	Strong transcription	Liver	Liver
48	chr3:105281400-105289400	Weak transcription	Osteobl	bone
49	chr3:105283000-105283800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr3:105283000-105285200	Enhancers	Rectal Mucosa Donor 31	rectum

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