Variant report

Variant	rs1199347
Chromosome Location	chr3:138083361-138083362
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:138073894..138077050-chr3:138080713..138083758,3	MCF-7	breast:
2	chr3:138081144..138083981-chr3:138086003..138087797,3	MCF-7	breast:
3	chr3:138071826..138074930-chr3:138082332..138084280,3	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1199328	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1199333	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1199334	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1199335	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1199336	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1199346	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1201763	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1209710	0.80[AMR][1000 genomes]
rs1212469	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13082471	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1308362	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1624314	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs166195	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs166196	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1679149	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1720825	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs183151	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs194146	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs253662	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs253666	0.80[AMR][1000 genomes]
rs40005	1.00[ASN][1000 genomes]
rs40412	1.00[ASN][1000 genomes]
rs42761	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4346503	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4437085	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4678416	0.94[EUR][1000 genomes]
rs6809480	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs774373	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs799328	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs811332	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][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	nsv530056	chr3:137312356-138161861	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv877537	chr3:137979007-138215114	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv530057	chr3:138014877-138734390	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv528349	chr3:138025396-138132393	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv1796956	chr3:138051423-138122781	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	esv1848610	chr3:138051423-138133412	Bivalent Enhancer Genic enhancers Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138068600-138084600	Weak transcription	Gastric	stomach
2	chr3:138068800-138093200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:138069200-138088200	Weak transcription	Fetal Lung	lung
4	chr3:138070000-138096600	Weak transcription	Fetal Brain Male	brain
5	chr3:138070200-138086400	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr3:138071000-138085600	Weak transcription	Brain Germinal Matrix	brain
7	chr3:138071200-138096600	Weak transcription	Aorta	Aorta
8	chr3:138071600-138086600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr3:138071800-138083400	Weak transcription	Placenta	Placenta
10	chr3:138073800-138084600	Weak transcription	Fetal Intestine Small	intestine
11	chr3:138074200-138095600	Enhancers	Fetal Heart	heart
12	chr3:138074800-138089800	Enhancers	Brain Cingulate Gyrus	brain
13	chr3:138075000-138086400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr3:138075000-138090000	Enhancers	Brain Anterior Caudate	brain
15	chr3:138075400-138087400	Enhancers	Right Atrium	heart
16	chr3:138075600-138089400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
17	chr3:138076000-138086400	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr3:138076000-138108200	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr3:138077800-138091600	Enhancers	Right Ventricle	heart
20	chr3:138078600-138086400	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr3:138078600-138100600	Weak transcription	NH-A	brain
22	chr3:138078800-138086600	Strong transcription	Fetal Stomach	stomach
23	chr3:138079000-138085400	Weak transcription	Colon Smooth Muscle	Colon
24	chr3:138079600-138095600	Weak transcription	Fetal Brain Female	brain
25	chr3:138079800-138086600	Weak transcription	Osteobl	bone
26	chr3:138080200-138086200	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr3:138080200-138096400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr3:138080600-138083600	Weak transcription	Lung	lung
29	chr3:138080600-138092000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:138080800-138083600	Enhancers	Brain Angular Gyrus	brain
31	chr3:138081000-138088400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr3:138081200-138084600	Weak transcription	Pancreas	Pancrea
33	chr3:138081200-138087000	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr3:138081600-138083400	Weak transcription	Fetal Muscle Trunk	muscle
35	chr3:138081600-138091000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr3:138081600-138108200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr3:138081800-138083400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr3:138081800-138083400	Weak transcription	HepG2	liver
39	chr3:138082200-138087400	Enhancers	Ovary	ovary
40	chr3:138082200-138088200	Genic enhancers	HSMMtube	muscle
41	chr3:138082400-138088800	Enhancers	Spleen	Spleen
42	chr3:138082400-138089400	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr3:138082800-138083400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
44	chr3:138082800-138083800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr3:138082800-138084400	Genic enhancers	Brain Substantia Nigra	brain
46	chr3:138082800-138088400	Genic enhancers	HSMM	muscle
47	chr3:138082800-138089400	Enhancers	Brain Hippocampus Middle	brain
48	chr3:138083000-138083600	Strong transcription	Fetal Muscle Leg	muscle
49	chr3:138083000-138083600	Strong transcription	Stomach Smooth Muscle	stomach
50	chr3:138083000-138083800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links