Variant report

Variant	rs11556604
Chromosome Location	chr3:119211384-119211385
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:119203935..119207565-chr3:119208359..119211450,3	MCF-7	breast:
2	chr3:119201366..119207142-chr3:119210949..119217240,7	K562	blood:
3	chr3:119201357..119202998-chr3:119210933..119213323,2	MCF-7	breast:
4	chr3:119205214..119207939-chr3:119209744..119211906,3	MCF-7	breast:
5	chr3:119207787..119212909-chr3:119213285..119218402,8	K562	blood:

Variant related genes	Relation type
ENSG00000272662	Chromatin interaction
ENSG00000163389	Chromatin interaction
ENSG00000113845	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1132202	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12631504	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12639070	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16829809	0.94[EUR][1000 genomes]
rs17281612	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17281647	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17281703	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2282173	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2282175	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs57509340	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs58968288	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59333081	0.92[EUR][1000 genomes]
rs59551807	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs60375691	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs60588168	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs60671082	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61740281	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6772534	0.93[EUR][1000 genomes]
rs6782411	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6800924	0.93[EUR][1000 genomes]
rs72968474	0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv829695	chr3:119178890-119367996	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119188400-119216200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:119188400-119216800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:119188600-119216200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:119188800-119216200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr3:119189000-119216200	Weak transcription	Stomach Mucosa	stomach
6	chr3:119189000-119216200	Weak transcription	HUVEC	blood vessel
7	chr3:119189000-119216600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:119189600-119211800	Strong transcription	Primary B cells from peripheral blood	blood
9	chr3:119189600-119211800	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr3:119189800-119211400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr3:119189800-119212200	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr3:119189800-119216000	Weak transcription	Fetal Heart	heart
13	chr3:119190000-119211800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr3:119190000-119212200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr3:119190000-119212200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr3:119190400-119212200	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr3:119190600-119211800	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr3:119190600-119212000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr3:119190800-119216400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr3:119191000-119216400	Weak transcription	Fetal Brain Male	brain
21	chr3:119192400-119216400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr3:119195800-119212000	Strong transcription	Liver	Liver
23	chr3:119196400-119216200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr3:119196400-119216600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr3:119196800-119216800	Weak transcription	Small Intestine	intestine
26	chr3:119197000-119216400	Weak transcription	Colon Smooth Muscle	Colon
27	chr3:119197400-119216600	Weak transcription	Aorta	Aorta
28	chr3:119202400-119211600	Strong transcription	GM12878-XiMat	blood
29	chr3:119202400-119211800	Strong transcription	Fetal Brain Female	brain
30	chr3:119202400-119212000	Strong transcription	Primary T cells from cord blood	blood
31	chr3:119202400-119213800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr3:119202600-119211800	Strong transcription	Duodenum Mucosa	Duodenum
33	chr3:119202800-119211800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr3:119202800-119211800	Strong transcription	Fetal Thymus	thymus
35	chr3:119203000-119211800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr3:119203000-119211800	Strong transcription	Fetal Muscle Trunk	muscle
37	chr3:119203000-119212000	Strong transcription	Primary hematopoietic stem cells	blood
38	chr3:119203200-119211800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr3:119204200-119212000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr3:119204200-119212200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:119204400-119211600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr3:119204400-119212000	Strong transcription	Fetal Muscle Leg	muscle
43	chr3:119204800-119216400	Weak transcription	Rectal Smooth Muscle	rectum
44	chr3:119205000-119216000	Weak transcription	Fetal Kidney	kidney
45	chr3:119205400-119216400	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr3:119205600-119216600	Weak transcription	Colonic Mucosa	Colon
47	chr3:119205600-119216600	Weak transcription	Esophagus	oesophagus
48	chr3:119205600-119216600	Weak transcription	Gastric	stomach
49	chr3:119205800-119216000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr3:119205800-119216200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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