Variant report

Variant	rs9990724
Chromosome Location	chr4:102103654-102103655
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10024318	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11943655	1.00[MEX][hapmap]
rs13435792	0.83[AMR][1000 genomes]
rs1441434	1.00[MEX][hapmap]
rs16996716	1.00[MEX][hapmap]
rs17030762	1.00[MEX][hapmap]
rs17030994	1.00[MEX][hapmap]
rs28406782	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28414287	1.00[EUR][1000 genomes]
rs28532678	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28599683	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28624713	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28678322	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3730250	1.00[MEX][hapmap];0.83[AMR][1000 genomes]
rs55633921	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57431778	0.85[AMR][1000 genomes]
rs6828770	1.00[MEX][hapmap]
rs6838341	1.00[ASW][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6851462	0.85[AMR][1000 genomes]
rs73833253	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73833255	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73833261	1.00[EUR][1000 genomes]
rs73833264	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73833265	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73833268	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73833269	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73833270	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73833271	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7653943	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7662565	1.00[EUR][1000 genomes]
rs7676124	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9686022	1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[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	nsv931418	chr4:101500167-102443207	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv999741	chr4:102009017-102454115	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
3	nsv537199	chr4:102009017-102454115	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1004766	chr4:102009017-102713765	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
5	nsv537200	chr4:102009017-102713765	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1011351	chr4:102056024-102450302	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:102079400-102113800	Weak transcription	Primary monocytes fromperipheralblood	blood
2	chr4:102090400-102103800	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr4:102090800-102112200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr4:102090800-102114400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr4:102093400-102103800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr4:102093600-102103800	Weak transcription	NHEK	skin
7	chr4:102093600-102105200	Weak transcription	NHLF	lung
8	chr4:102094400-102103800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr4:102094400-102108600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr4:102096200-102112600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr4:102096600-102112000	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr4:102096600-102112000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr4:102096600-102112000	Weak transcription	Right Ventricle	heart
14	chr4:102096800-102108000	Weak transcription	Brain Hippocampus Middle	brain
15	chr4:102097400-102112200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr4:102097600-102105000	Weak transcription	Duodenum Mucosa	Duodenum
17	chr4:102097800-102108200	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr4:102097800-102112200	Weak transcription	Adipose Nuclei	Adipose
19	chr4:102097800-102112200	Weak transcription	Left Ventricle	heart
20	chr4:102097800-102112600	Weak transcription	Pancreas	Pancrea
21	chr4:102098600-102104400	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr4:102098600-102109800	Weak transcription	HepG2	liver
23	chr4:102098600-102118600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr4:102099000-102107800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr4:102099800-102107800	Weak transcription	Brain Anterior Caudate	brain
26	chr4:102100000-102104800	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr4:102100200-102104800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr4:102100400-102103800	Weak transcription	Primary T cells from cord blood	blood
29	chr4:102100600-102104400	Weak transcription	Osteobl	bone
30	chr4:102100800-102104800	Weak transcription	A549	lung
31	chr4:102100800-102105400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr4:102101400-102104800	Weak transcription	NHDF-Ad	bronchial
33	chr4:102101400-102105000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr4:102101800-102103800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr4:102101800-102108600	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr4:102102000-102109800	Weak transcription	Esophagus	oesophagus
37	chr4:102102000-102112200	Weak transcription	Psoas Muscle	Psoas
38	chr4:102102000-102112800	Weak transcription	Right Atrium	heart
39	chr4:102102200-102110600	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr4:102102200-102112200	Weak transcription	Aorta	Aorta
41	chr4:102102200-102116400	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr4:102102800-102105000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr4:102103000-102104000	Weak transcription	Fetal Muscle Leg	muscle
44	chr4:102103200-102104000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr4:102103200-102104600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
46	chr4:102103400-102103800	Weak transcription	Fetal Intestine Large	intestine
47	chr4:102103400-102104000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr4:102103400-102104000	Strong transcription	Primary B cells from cord blood	blood
49	chr4:102103400-102104200	Strong transcription	Primary B cells from peripheral blood	blood
50	chr4:102103400-102104200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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