Variant report

Variant	rs1713954
Chromosome Location	chr4:57924358-57924359
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10031585	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11947115	0.82[EUR][1000 genomes]
rs1277297	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1713953	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1713955	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1713956	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1713958	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1713959	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1713960	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1718834	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs4561981	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6848820	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7663219	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7673762	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs7698085	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1713954	IGFBP7	cis	multi-tissue	Pritchard
rs1713954	IGFBP7	cis	parietal	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57899400-57925000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr4:57899600-57942200	Weak transcription	Primary hematopoietic stem cells	blood
3	chr4:57915800-57930200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr4:57917600-57931000	Weak transcription	Pancreas	Pancrea
5	chr4:57917800-57926000	Weak transcription	Fetal Kidney	kidney
6	chr4:57918000-57929000	Weak transcription	HUVEC	blood vessel
7	chr4:57918600-57929200	Weak transcription	Fetal Muscle Leg	muscle
8	chr4:57918600-57936800	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr4:57920400-57925600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr4:57920400-57926200	Weak transcription	A549	lung
11	chr4:57920400-57930200	Weak transcription	Lung	lung
12	chr4:57920600-57924400	Strong transcription	Muscle Satellite Cultured Cells	--
13	chr4:57920600-57927600	Weak transcription	HMEC	breast
14	chr4:57921000-57926800	Weak transcription	Small Intestine	intestine
15	chr4:57921000-57931000	Weak transcription	NHEK	skin
16	chr4:57921200-57924800	Enhancers	Right Ventricle	heart
17	chr4:57921800-57928200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr4:57922000-57926200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr4:57922800-57931200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr4:57923000-57926200	Weak transcription	NHLF	lung
21	chr4:57923000-57928600	Weak transcription	Psoas Muscle	Psoas
22	chr4:57923000-57929200	Weak transcription	Brain Hippocampus Middle	brain
23	chr4:57923000-57930200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr4:57923000-57931000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr4:57923000-57931800	Weak transcription	Duodenum Mucosa	Duodenum
26	chr4:57923000-57932000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr4:57923200-57926400	Weak transcription	NH-A	brain
28	chr4:57923400-57926600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr4:57923400-57926800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr4:57923600-57924400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr4:57923600-57928800	Weak transcription	Fetal Lung	lung
32	chr4:57923800-57926800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr4:57923800-57937200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr4:57924000-57926200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr4:57924000-57929400	Weak transcription	Brain Anterior Caudate	brain
36	chr4:57924000-57929800	Weak transcription	Fetal Stomach	stomach
37	chr4:57924000-57931200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr4:57924200-57924600	Strong transcription	HSMMtube	muscle
39	chr4:57924200-57925800	Weak transcription	Osteobl	bone
40	chr4:57924200-57926000	Weak transcription	Rectal Smooth Muscle	rectum
41	chr4:57924200-57926200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr4:57924200-57926200	Weak transcription	Aorta	Aorta
43	chr4:57924200-57926200	Weak transcription	Colon Smooth Muscle	Colon
44	chr4:57924200-57926600	Weak transcription	Stomach Smooth Muscle	stomach
45	chr4:57924200-57926800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr4:57924200-57926800	Weak transcription	Ovary	ovary
47	chr4:57924200-57927000	Weak transcription	Left Ventricle	heart
48	chr4:57924200-57927200	Weak transcription	HSMM	muscle
49	chr4:57924200-57927600	Weak transcription	Right Atrium	heart
50	chr4:57924200-57927800	Weak transcription	Fetal Heart	heart

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