Variant report

Variant	rs4894832
Chromosome Location	chr3:105267756-105267757
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs17189452	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3772551	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3772554	1.00[CEU][hapmap];0.89[YRI][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs478259	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]
rs485922	1.00[CEU][hapmap];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs490029	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs519016	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs526375	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs526963	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs562960	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs577295	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs610047	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs620165	0.92[ASN][1000 genomes]
rs629187	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.91[EUR][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	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
6	nsv1008291	chr3:105261480-105272449	Strong transcription Weak transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4894832	ALCAM	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:85 , 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	chr3:105223800-105274800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:105232200-105274000	Weak transcription	HSMMtube	muscle
4	chr3:105234600-105274600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr3:105237800-105274600	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr3:105237800-105275800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr3:105242000-105293600	Weak transcription	Lung	lung
8	chr3:105242400-105280400	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr3:105244800-105275800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr3:105245800-105268000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr3:105246600-105284400	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr3:105248000-105281200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr3:105248400-105291200	Weak transcription	Brain Cingulate Gyrus	brain
14	chr3:105249400-105278600	Weak transcription	Small Intestine	intestine
15	chr3:105249800-105284000	Weak transcription	Fetal Stomach	stomach
16	chr3:105249800-105285200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr3:105250600-105270400	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr3:105251800-105274400	Weak transcription	Dnd41	blood
19	chr3:105253200-105273000	Weak transcription	Gastric	stomach
20	chr3:105253800-105270000	Weak transcription	Fetal Intestine Large	intestine
21	chr3:105254000-105273000	Weak transcription	Fetal Lung	lung
22	chr3:105254800-105279800	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr3:105256200-105268200	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr3:105257200-105269400	Weak transcription	Fetal Heart	heart
25	chr3:105257400-105272400	Weak transcription	NHDF-Ad	bronchial
26	chr3:105257800-105271400	Weak transcription	Stomach Mucosa	stomach
27	chr3:105258000-105270200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr3:105258000-105274600	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr3:105258200-105268400	Strong transcription	GM12878-XiMat	blood
30	chr3:105258600-105273600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr3:105258800-105271800	Strong transcription	HUVEC	blood vessel
32	chr3:105258800-105274400	Strong transcription	Liver	Liver
33	chr3:105258800-105274400	Strong transcription	NH-A	brain
34	chr3:105259000-105271200	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr3:105259000-105273400	Strong transcription	Osteobl	bone
36	chr3:105259200-105269000	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr3:105259400-105272200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr3:105259400-105272400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr3:105259400-105272600	Strong transcription	Muscle Satellite Cultured Cells	--
40	chr3:105259400-105274000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr3:105259400-105274200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr3:105259400-105281200	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr3:105259800-105272400	Weak transcription	Brain Hippocampus Middle	brain
44	chr3:105260000-105269800	Weak transcription	Psoas Muscle	Psoas
45	chr3:105260400-105268000	Strong transcription	HSMM	muscle
46	chr3:105260400-105268400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr3:105260800-105297000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr3:105260800-105299800	Weak transcription	Pancreas	Pancrea
49	chr3:105261600-105269400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr3:105261800-105269200	Weak transcription	NHEK	skin

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