Variant report

Variant	rs1700
Chromosome Location	chr3:120114637-120114638
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10048964	0.83[EUR][1000 genomes]
rs1147681	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1147688	0.84[CEU][hapmap];0.92[GIH][hapmap];0.81[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1147689	0.84[CEU][hapmap];0.85[GIH][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1147690	0.83[CEU][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1147697	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11914405	0.83[EUR][1000 genomes]
rs11928731	0.83[EUR][1000 genomes]
rs1625178	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1716855	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1716856	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1733326	0.84[CEU][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1733328	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2638597	0.84[CEU][hapmap];0.92[GIH][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs28487977	0.83[EUR][1000 genomes]
rs28535957	0.83[EUR][1000 genomes]
rs28718940	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28826066	0.83[EUR][1000 genomes]
rs6764516	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs6767308	0.84[CEU][hapmap];0.85[GIH][hapmap];0.82[EUR][1000 genomes]
rs6777979	0.84[CEU][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6799005	1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6808913	0.83[EUR][1000 genomes]
rs787187	0.85[AMR][1000 genomes]
rs787193	0.85[AMR][1000 genomes]
rs787205	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs787206	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs923729	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs951658	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs9810151	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9810784	0.83[EUR][1000 genomes]
rs9822636	0.83[EUR][1000 genomes]
rs9822759	0.83[EUR][1000 genomes]
rs9851711	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9856670	0.83[EUR][1000 genomes]
rs9860676	1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9876547	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv877376	chr3:119824037-120119446	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1007557	chr3:119892894-120764353	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv536706	chr3:119892894-120764353	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv829698	chr3:119960869-120129126	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats 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 miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv1012127	chr3:120015620-120272893	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active 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 miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv536707	chr3:120015620-120272893	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
8	nsv1006428	chr3:120015620-120421982	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	esv3369381	chr3:120066425-120425510	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
10	esv3350409	chr3:120066445-120425480	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1700	RABL3	cis	cerebellum	SCAN
rs1700	B4GALT4	cis	parietal	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120107000-120115200	Weak transcription	Spleen	Spleen
2	chr3:120107000-120118200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:120110000-120118200	Weak transcription	Esophagus	oesophagus
4	chr3:120111000-120114800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr3:120111400-120115200	Weak transcription	A549	lung
6	chr3:120111400-120115400	Weak transcription	Brain Hippocampus Middle	brain
7	chr3:120111600-120114800	Weak transcription	Fetal Intestine Small	intestine
8	chr3:120111800-120115200	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr3:120112000-120115400	Weak transcription	Brain Germinal Matrix	brain
10	chr3:120112000-120123600	Strong transcription	Osteobl	bone
11	chr3:120112000-120123800	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr3:120112000-120132600	Strong transcription	Placenta Amnion	Placenta Amnion
13	chr3:120112200-120123600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr3:120112200-120124000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr3:120112200-120124000	Strong transcription	HSMM	muscle
16	chr3:120112200-120127400	Strong transcription	Left Ventricle	heart
17	chr3:120112200-120130000	Strong transcription	Fetal Muscle Trunk	muscle
18	chr3:120112200-120131400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr3:120112200-120132600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr3:120112400-120114800	Genic enhancers	Colon Smooth Muscle	Colon
21	chr3:120112400-120123600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr3:120112400-120123800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr3:120112400-120123800	Strong transcription	Muscle Satellite Cultured Cells	--
24	chr3:120112400-120129600	Strong transcription	Stomach Smooth Muscle	stomach
25	chr3:120112400-120130200	Strong transcription	Adipose Nuclei	Adipose
26	chr3:120112400-120132600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr3:120112400-120132600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr3:120112400-120132600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr3:120112400-120132600	Strong transcription	HSMMtube	muscle
30	chr3:120112400-120132600	Strong transcription	NH-A	brain
31	chr3:120112400-120132600	Strong transcription	NHDF-Ad	bronchial
32	chr3:120112400-120132600	Strong transcription	NHLF	lung
33	chr3:120112600-120115200	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr3:120112600-120115800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr3:120112600-120122600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr3:120112600-120123000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr3:120112600-120130600	Strong transcription	Ovary	ovary
38	chr3:120112600-120131400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr3:120112600-120132400	Strong transcription	Cortex derived primary cultured neurospheres	brain
40	chr3:120112600-120132400	Strong transcription	Aorta	Aorta
41	chr3:120112600-120132600	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr3:120112600-120132600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr3:120112600-120132800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr3:120112800-120115200	Weak transcription	Brain Substantia Nigra	brain
45	chr3:120112800-120115200	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr3:120112800-120116800	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr3:120112800-120123600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr3:120112800-120131200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr3:120112800-120132000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr3:120112800-120132600	Strong transcription	HUES48 Cell Line	embryonic stem cell

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