Variant report

Variant	rs3822830
Chromosome Location	chr5:128434936-128434937
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:128429058..128432172-chr5:128432458..128435695,7	MCF-7	breast:
2	chr5:128426917..128432397-chr5:128432508..128439991,15	K562	blood:
3	chr5:128433582..128436325-chr5:128460643..128463570,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000066583	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10036277	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10058170	0.80[AMR][1000 genomes]
rs10071265	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1127827	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1181955	0.81[EUR][1000 genomes]
rs11960471	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13181777	0.80[EUR][1000 genomes]
rs2112697	0.86[AMR][1000 genomes]
rs2161403	0.83[AMR][1000 genomes]
rs2194149	0.82[AMR][1000 genomes]
rs2312251	0.96[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2430194	0.96[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2430195	0.96[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs257911	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs257912	0.95[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs257919	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3798115	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3798116	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3798117	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3798120	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3822832	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4141014	0.81[EUR][1000 genomes]
rs4836444	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs58498861	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6595879	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6595885	0.83[AMR][1000 genomes]
rs6867600	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6868228	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6871	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6881138	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6888909	1.00[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7714427	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7733245	0.82[AMR][1000 genomes]
rs963677	0.84[AMR][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	nsv830485	chr5:128298622-128480492	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
2	nsv882842	chr5:128301971-128552706	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
3	nsv599701	chr5:128328165-128773052	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
4	nsv1015525	chr5:128335133-128443859	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
5	nsv882847	chr5:128368505-128665719	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
6	nsv882848	chr5:128378225-128516629	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:128431200-128447800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:128431400-128443600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr5:128431400-128450600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr5:128431400-128457400	Weak transcription	Lung	lung
5	chr5:128431600-128435200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr5:128431600-128435200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr5:128431600-128435600	Enhancers	Fetal Lung	lung
8	chr5:128431600-128441200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr5:128431600-128441200	Weak transcription	Fetal Kidney	kidney
10	chr5:128431600-128442000	Weak transcription	Primary B cells from peripheral blood	blood
11	chr5:128431600-128442000	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr5:128431600-128442600	Weak transcription	Thymus	Thymus
13	chr5:128431600-128444000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr5:128431600-128446000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr5:128431600-128446400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr5:128431600-128450400	Weak transcription	Placenta	Placenta
17	chr5:128431600-128450400	Weak transcription	HSMM	muscle
18	chr5:128431600-128454200	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr5:128431800-128441600	Weak transcription	Primary B cells from cord blood	blood
20	chr5:128431800-128446400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr5:128432200-128435000	Enhancers	Brain Substantia Nigra	brain
22	chr5:128432200-128442400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr5:128432200-128442600	Weak transcription	A549	lung
24	chr5:128432200-128442800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr5:128432200-128450400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr5:128432200-128454600	Weak transcription	Aorta	Aorta
27	chr5:128432400-128441200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr5:128432400-128442200	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr5:128432400-128442600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr5:128432400-128442600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr5:128432400-128446000	Weak transcription	HMEC	breast
32	chr5:128432400-128450400	Weak transcription	Brain Angular Gyrus	brain
33	chr5:128432600-128441000	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr5:128432600-128442200	Weak transcription	Fetal Muscle Trunk	muscle
35	chr5:128432600-128442600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr5:128432800-128435200	Enhancers	Ovary	ovary
37	chr5:128432800-128441200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr5:128433000-128435200	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr5:128433200-128435000	Enhancers	Primary T helper cells PMA-I stimulated	--
40	chr5:128433200-128435800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr5:128433200-128435800	Enhancers	Psoas Muscle	Psoas
42	chr5:128433400-128435200	Enhancers	Pancreas	Pancrea
43	chr5:128433400-128435400	Enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr5:128433400-128435800	Enhancers	Skeletal Muscle Female	skeletal muscle
45	chr5:128433400-128435800	Enhancers	Stomach Mucosa	stomach
46	chr5:128433400-128453800	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr5:128433600-128435000	Flanking Active TSS	Adipose Nuclei	Adipose
48	chr5:128433600-128435200	Enhancers	Fetal Thymus	thymus
49	chr5:128433800-128435200	Enhancers	Primary neutrophils fromperipheralblood	blood
50	chr5:128433800-128435200	Enhancers	HUVEC	blood vessel

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links