Variant report

Variant	rs16860709
Chromosome Location	chr3:112970707-112970708
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1499898	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16845106	1.00[CEU][hapmap];0.81[JPT][hapmap];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16860720	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16860770	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17256551	1.00[TSI][hapmap]
rs17320040	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17320242	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2399476	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34600669	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35536878	0.81[AFR][1000 genomes]
rs3814399	0.88[CHB][hapmap];0.94[CHD][hapmap];0.82[JPT][hapmap]
rs41271353	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57104308	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57661011	0.95[AFR][1000 genomes]
rs59388346	0.93[AFR][1000 genomes]
rs59590258	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60070011	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61035513	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6792692	0.85[YRI][hapmap];0.81[AFR][1000 genomes]
rs9820139	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9832953	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9849714	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9855011	1.00[ASN][1000 genomes]
rs9872998	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9878424	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs998647	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs999365	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.95[ASN][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	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv829677	chr3:112857075-113038987	Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv1003511	chr3:112858775-112989045	Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
5	nsv877348	chr3:112914756-113012509	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112932000-112972800	Weak transcription	Aorta	Aorta
2	chr3:112961600-112983000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:112962800-112972400	Weak transcription	Brain Germinal Matrix	brain
4	chr3:112963000-112972800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr3:112964600-112971400	Enhancers	HSMMtube	muscle
6	chr3:112966200-112972400	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr3:112966800-112972600	Weak transcription	Duodenum Mucosa	Duodenum
8	chr3:112966800-112973600	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr3:112967000-112972400	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr3:112967200-112972200	Weak transcription	Fetal Thymus	thymus
11	chr3:112967200-112973200	Weak transcription	Colonic Mucosa	Colon
12	chr3:112967200-112973200	Weak transcription	Right Atrium	heart
13	chr3:112967400-112972600	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr3:112967400-112972600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr3:112967400-112972600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr3:112968000-112971400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr3:112968000-112973200	Weak transcription	Left Ventricle	heart
18	chr3:112968200-112972400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr3:112968200-112972400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:112968200-112972400	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr3:112968400-112971400	Strong transcription	Fetal Stomach	stomach
22	chr3:112968400-112972400	Weak transcription	Fetal Brain Male	brain
23	chr3:112968400-112973000	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr3:112968600-112971000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr3:112968600-112971000	Strong transcription	Fetal Lung	lung
26	chr3:112968600-112971400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr3:112968600-112971400	Strong transcription	Brain Anterior Caudate	brain
28	chr3:112968600-112971400	Strong transcription	Fetal Kidney	kidney
29	chr3:112968600-112972000	Genic enhancers	Cortex derived primary cultured neurospheres	brain
30	chr3:112968600-112972400	Strong transcription	Fetal Intestine Small	intestine
31	chr3:112968600-112972600	Weak transcription	Brain Angular Gyrus	brain
32	chr3:112968600-112980000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr3:112968800-112971200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr3:112968800-112971200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr3:112968800-112971200	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr3:112968800-112971200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr3:112968800-112971400	Strong transcription	Adipose Nuclei	Adipose
38	chr3:112968800-112971800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr3:112968800-112972400	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr3:112968800-112972600	Weak transcription	Brain Hippocampus Middle	brain
41	chr3:112968800-112973200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr3:112968800-112973400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr3:112969000-112971000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr3:112969000-112971200	Strong transcription	Brain Cingulate Gyrus	brain
45	chr3:112969000-112971600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr3:112969000-112971800	Strong transcription	Placenta Amnion	Placenta Amnion
47	chr3:112969000-112995200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr3:112969200-112971400	Strong transcription	Rectal Smooth Muscle	rectum
49	chr3:112969200-112971600	Strong transcription	Stomach Smooth Muscle	stomach
50	chr3:112969200-112971800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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