Variant report

Variant	rs16851279
Chromosome Location	chr3:105266274-105266275
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs16851098	0.84[MEX][hapmap]
rs2062433	0.89[AMR][1000 genomes]
rs2291377	0.82[ASW][hapmap];1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.89[YRI][hapmap];0.89[AMR][1000 genomes]
rs2291378	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.89[YRI][hapmap];0.89[AMR][1000 genomes]
rs3772555	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3821492	0.85[MEX][hapmap];0.89[TSI][hapmap]
rs62260777	0.89[AMR][1000 genomes]
rs62262966	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262967	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262968	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7624892	0.89[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv963527	chr3:105259211-105267049	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv1008291	chr3:105261480-105272449	Strong transcription Weak transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 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	chr3:105242800-105266800	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr3:105244800-105275800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr3:105245800-105268000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr3:105246600-105284400	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr3:105248000-105281200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr3:105248400-105291200	Weak transcription	Brain Cingulate Gyrus	brain
15	chr3:105249400-105278600	Weak transcription	Small Intestine	intestine
16	chr3:105249800-105284000	Weak transcription	Fetal Stomach	stomach
17	chr3:105249800-105285200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr3:105250600-105270400	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr3:105251200-105266400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr3:105251800-105274400	Weak transcription	Dnd41	blood
21	chr3:105253200-105273000	Weak transcription	Gastric	stomach
22	chr3:105253800-105270000	Weak transcription	Fetal Intestine Large	intestine
23	chr3:105254000-105273000	Weak transcription	Fetal Lung	lung
24	chr3:105254800-105279800	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr3:105256200-105268200	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr3:105257200-105269400	Weak transcription	Fetal Heart	heart
27	chr3:105257400-105272400	Weak transcription	NHDF-Ad	bronchial
28	chr3:105257800-105271400	Weak transcription	Stomach Mucosa	stomach
29	chr3:105258000-105270200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr3:105258000-105274600	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr3:105258200-105268400	Strong transcription	GM12878-XiMat	blood
32	chr3:105258600-105273600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr3:105258800-105266600	Strong transcription	Primary B cells from peripheral blood	blood
34	chr3:105258800-105267000	Strong transcription	Primary B cells from cord blood	blood
35	chr3:105258800-105271800	Strong transcription	HUVEC	blood vessel
36	chr3:105258800-105274400	Strong transcription	Liver	Liver
37	chr3:105258800-105274400	Strong transcription	NH-A	brain
38	chr3:105259000-105271200	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr3:105259000-105273400	Strong transcription	Osteobl	bone
40	chr3:105259200-105269000	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr3:105259400-105272200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr3:105259400-105272400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr3:105259400-105272600	Strong transcription	Muscle Satellite Cultured Cells	--
44	chr3:105259400-105274000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr3:105259400-105274200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr3:105259400-105281200	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr3:105259600-105266600	Weak transcription	Ovary	ovary
48	chr3:105259800-105272400	Weak transcription	Brain Hippocampus Middle	brain
49	chr3:105260000-105269800	Weak transcription	Psoas Muscle	Psoas
50	chr3:105260400-105266600	Strong transcription	A549	lung

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