Variant report

Variant	rs3733409
Chromosome Location	chr4:187627593-187627594
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:187605170..187608149-chr4:187626258..187628556,2	MCF-7	breast:
2	chr4:187627017..187629232-chr4:187633048..187634644,2	MCF-7	breast:
3	chr4:187625004..187626808-chr4:187627484..187629587,2	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs162182	0.80[CHB][hapmap]
rs167854	0.81[CHB][hapmap]
rs17077740	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2017933	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs327067	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs327078	0.80[CHB][hapmap]
rs327093	0.82[EUR][1000 genomes]
rs327100	0.84[EUR][1000 genomes]
rs327102	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs327111	0.87[CHB][hapmap]
rs3733415	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs456000	0.81[CHB][hapmap]
rs462509	0.87[CHB][hapmap]
rs59035714	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6818461	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73015642	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73015656	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73015660	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73015670	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025088	chr4:187407683-187674585	Genic enhancers Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1025244	chr4:187419770-188284813	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv1034212	chr4:187437895-188030805	Weak transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv537438	chr4:187437895-188030805	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv532745	chr4:187471692-188205443	Bivalent/Poised TSS Weak transcription Genic enhancers Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	nsv1022262	chr4:187475862-187848284	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv1024705	chr4:187534005-187849091	Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv1026970	chr4:187537418-187913351	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv596440	chr4:187538133-187848075	Genic enhancers Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:187608000-187632400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr4:187614800-187629400	Weak transcription	Esophagus	oesophagus
3	chr4:187615400-187628000	Weak transcription	K562	blood
4	chr4:187620000-187628800	Weak transcription	Small Intestine	intestine
5	chr4:187621200-187628200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr4:187622600-187634200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr4:187622800-187630400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr4:187623000-187628000	Weak transcription	Brain Hippocampus Middle	brain
9	chr4:187623200-187627600	Enhancers	Colon Smooth Muscle	Colon
10	chr4:187623200-187631800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr4:187623200-187632000	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr4:187623400-187627600	Enhancers	Fetal Heart	heart
13	chr4:187623400-187627800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr4:187623400-187628000	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr4:187623400-187628000	Genic enhancers	HepG2	liver
16	chr4:187623400-187628200	Weak transcription	Gastric	stomach
17	chr4:187623400-187630000	Weak transcription	Right Atrium	heart
18	chr4:187623400-187630200	Weak transcription	Placenta	Placenta
19	chr4:187623400-187632800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr4:187623600-187630200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr4:187623800-187629200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr4:187623800-187630000	Weak transcription	Right Ventricle	heart
23	chr4:187623800-187631600	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr4:187624000-187632000	Weak transcription	Brain Anterior Caudate	brain
25	chr4:187624200-187627600	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr4:187624400-187627800	Weak transcription	Fetal Kidney	kidney
27	chr4:187624400-187630200	Weak transcription	Brain Angular Gyrus	brain
28	chr4:187624400-187631000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr4:187624600-187628000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr4:187624600-187629000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr4:187624800-187633800	Weak transcription	Brain Substantia Nigra	brain
32	chr4:187625000-187628000	Weak transcription	Brain Germinal Matrix	brain
33	chr4:187625000-187628000	Weak transcription	Colonic Mucosa	Colon
34	chr4:187625000-187628000	Weak transcription	Ovary	ovary
35	chr4:187625000-187631800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr4:187625400-187627800	Weak transcription	Adipose Nuclei	Adipose
37	chr4:187625400-187631000	Strong transcription	HMEC	breast
38	chr4:187625800-187630800	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr4:187625800-187631000	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr4:187626000-187627800	Enhancers	Aorta	Aorta
41	chr4:187626000-187627800	Weak transcription	Liver	Liver
42	chr4:187626200-187627800	Enhancers	Left Ventricle	heart
43	chr4:187626200-187630000	Strong transcription	Duodenum Mucosa	Duodenum
44	chr4:187626200-187630000	Strong transcription	Fetal Intestine Small	intestine
45	chr4:187626200-187630200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr4:187626200-187631000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr4:187626200-187631000	Strong transcription	Fetal Intestine Large	intestine
48	chr4:187626200-187631000	Strong transcription	NH-A	brain
49	chr4:187626400-187630800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr4:187626400-187631000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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