Variant report

Variant	rs1009248
Chromosome Location	chr3:120063949-120063950
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:120059782..120066077-chr3:120066537..120070898,10	K562	blood:

Variant related genes	Relation type
ENSG00000240661	Chromatin interaction
ENSG00000163428	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10511400	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1085615	0.84[ASN][1000 genomes]
rs12495760	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16831033	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16831036	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2319674	0.94[ASN][1000 genomes]
rs2943757	0.89[ASN][1000 genomes]
rs34104182	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58556686	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6438577	0.94[ASN][1000 genomes]
rs6770482	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6782419	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6791815	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6803206	0.94[ASN][1000 genomes]
rs6803428	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6806659	0.94[ASN][1000 genomes]
rs701988	0.94[ASN][1000 genomes]
rs72956871	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73855212	0.83[ASN][1000 genomes]
rs7632516	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs787191	0.84[ASN][1000 genomes]
rs787195	0.84[ASN][1000 genomes]
rs787209	0.84[ASN][1000 genomes]
rs9817398	0.98[ASN][1000 genomes]
rs9822269	0.98[ASN][1000 genomes]
rs9822672	0.98[ASN][1000 genomes]
rs9874631	0.94[ASN][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	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	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
9	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
10	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

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120026800-120067200	Weak transcription	Aorta	Aorta
2	chr3:120033200-120067000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:120044400-120066800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr3:120045200-120066800	Weak transcription	Stomach Mucosa	stomach
5	chr3:120045600-120066800	Weak transcription	Colonic Mucosa	Colon
6	chr3:120048400-120066800	Weak transcription	Right Ventricle	heart
7	chr3:120050400-120066000	Weak transcription	Fetal Brain Male	brain
8	chr3:120051000-120067000	Weak transcription	Esophagus	oesophagus
9	chr3:120051200-120065600	Weak transcription	HMEC	breast
10	chr3:120051200-120066800	Weak transcription	Psoas Muscle	Psoas
11	chr3:120051200-120066800	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr3:120051800-120065600	Weak transcription	Brain Angular Gyrus	brain
13	chr3:120052600-120067000	Weak transcription	Left Ventricle	heart
14	chr3:120052800-120064400	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr3:120053200-120065200	Weak transcription	Stomach Smooth Muscle	stomach
16	chr3:120053200-120066600	Weak transcription	Fetal Kidney	kidney
17	chr3:120053800-120066600	Weak transcription	Rectal Smooth Muscle	rectum
18	chr3:120053800-120066600	Weak transcription	NH-A	brain
19	chr3:120054000-120066000	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr3:120054200-120064600	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr3:120054200-120065600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr3:120054200-120065600	Weak transcription	Fetal Heart	heart
23	chr3:120054200-120065600	Weak transcription	NHEK	skin
24	chr3:120054200-120066600	Weak transcription	HUVEC	blood vessel
25	chr3:120054200-120066600	Weak transcription	K562	blood
26	chr3:120055200-120064200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr3:120057800-120067000	Weak transcription	Small Intestine	intestine
28	chr3:120058400-120065600	Weak transcription	Brain Substantia Nigra	brain
29	chr3:120058400-120065800	Weak transcription	Brain Anterior Caudate	brain
30	chr3:120058600-120065200	Weak transcription	Adipose Nuclei	Adipose
31	chr3:120058600-120065800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr3:120058600-120066600	Weak transcription	Fetal Lung	lung
33	chr3:120058800-120064800	Weak transcription	Fetal Brain Female	brain
34	chr3:120059000-120065000	Weak transcription	Brain Cingulate Gyrus	brain
35	chr3:120059000-120066800	Weak transcription	Placenta	Placenta
36	chr3:120060800-120066600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr3:120061000-120065200	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr3:120061000-120066600	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr3:120061200-120066400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr3:120061200-120066600	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr3:120061400-120064400	Weak transcription	Ovary	ovary
42	chr3:120061400-120064800	Weak transcription	Lung	lung
43	chr3:120061400-120065200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr3:120061400-120066800	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr3:120061400-120066800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr3:120061400-120066800	Weak transcription	Gastric	stomach
47	chr3:120061400-120067000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr3:120061600-120065600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr3:120061600-120066400	Weak transcription	Pancreas	Pancrea
50	chr3:120061600-120066600	Weak transcription	iPS-18 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links