Variant report

Variant	rs16877612
Chromosome Location	chr5:79515288-79515289
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:79503625..79505476-chr5:79514776..79516793,2	MCF-7	breast:
2	chr5:79514935..79516719-chr5:79517338..79519015,2	MCF-7	breast:
3	chr5:79507637..79510156-chr5:79513489..79515447,2	K562	blood:

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10036776	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10055268	0.99[ASN][1000 genomes]
rs10061215	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4235717	0.99[ASN][1000 genomes]
rs4703805	0.87[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];0.85[TSI][hapmap];0.91[ASN][1000 genomes]
rs60316437	0.91[ASN][1000 genomes]
rs6879270	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432748	chr5:79300434-79577760	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 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	chr5:79498600-79520800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr5:79498600-79521200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr5:79499000-79517800	Weak transcription	Aorta	Aorta
4	chr5:79500000-79537600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr5:79501600-79516800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr5:79502000-79516200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr5:79506400-79516400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr5:79507000-79516400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr5:79508600-79516200	Weak transcription	Colonic Mucosa	Colon
10	chr5:79509400-79516000	Weak transcription	Fetal Intestine Large	intestine
11	chr5:79509600-79525600	Weak transcription	Spleen	Spleen
12	chr5:79509800-79516600	Weak transcription	Duodenum Mucosa	Duodenum
13	chr5:79509800-79535600	Weak transcription	Primary B cells from cord blood	blood
14	chr5:79510800-79517400	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr5:79511000-79518200	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr5:79511200-79515400	Enhancers	Fetal Thymus	thymus
17	chr5:79511200-79517400	Enhancers	Brain Cingulate Gyrus	brain
18	chr5:79511600-79515600	Enhancers	Sigmoid Colon	Sigmoid Colon
19	chr5:79511800-79516200	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr5:79512000-79534000	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr5:79512200-79516000	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr5:79512400-79516000	Enhancers	Primary T cells fromperipheralblood	blood
23	chr5:79512400-79516200	Weak transcription	Small Intestine	intestine
24	chr5:79512400-79516400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
25	chr5:79513000-79516400	Enhancers	Colon Smooth Muscle	Colon
26	chr5:79513000-79516800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr5:79513000-79517000	Enhancers	Left Ventricle	heart
28	chr5:79513200-79515600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr5:79513200-79515600	Enhancers	iPS-15b Cell Line	embryonic stem cell
30	chr5:79513200-79515600	Enhancers	NHEK	skin
31	chr5:79513200-79515800	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr5:79513200-79516800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr5:79513200-79516800	Enhancers	Fetal Lung	lung
34	chr5:79513200-79517000	Enhancers	Stomach Mucosa	stomach
35	chr5:79513200-79518000	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr5:79513400-79516400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr5:79513400-79516800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
38	chr5:79513400-79516800	Enhancers	Brain Substantia Nigra	brain
39	chr5:79513400-79519600	Weak transcription	HMEC	breast
40	chr5:79513600-79515600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr5:79513600-79516400	Enhancers	Liver	Liver
42	chr5:79513600-79516800	Enhancers	Brain Angular Gyrus	brain
43	chr5:79513600-79517400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr5:79513600-79518200	Enhancers	Brain Hippocampus Middle	brain
45	chr5:79513600-79525400	Weak transcription	Adipose Nuclei	Adipose
46	chr5:79513800-79515400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr5:79513800-79516400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr5:79513800-79517000	Enhancers	Brain Anterior Caudate	brain
49	chr5:79513800-79517000	Enhancers	Brain Inferior Temporal Lobe	brain
50	chr5:79513800-79517200	Weak transcription	iPS-18 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links