Variant report

Variant	rs605654
Chromosome Location	chr10:116155850-116155851
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:116151670..116155313-chr10:116155442..116158491,3	MCF-7	breast:
2	chr10:116154812..116157671-chr10:116168139..116169677,2	MCF-7	breast:
3	chr10:116151729..116154077-chr10:116154696..116157816,3	K562	blood:

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

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11196728	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11196738	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11196750	0.91[CEU][hapmap]
rs12354693	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12354943	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12355335	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12356147	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12357098	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12359269	0.90[CEU][hapmap];0.85[CHB][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12573832	0.90[CEU][hapmap]
rs17406965	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs41293058	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs475150	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61868314	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61868324	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs622320	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs622646	1.00[CEU][hapmap];0.85[CHB][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6585277	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6585283	0.89[CEU][hapmap]
rs7069926	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7900888	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7910088	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7916374	1.00[CEU][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7916796	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs941855	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9665297	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037308	chr10:116141946-116519765	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer 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
2	nsv540780	chr10:116141946-116519765	Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:116134000-116157600	Weak transcription	Colonic Mucosa	Colon
2	chr10:116146400-116157000	Enhancers	HMEC	breast
3	chr10:116149000-116160000	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr10:116151600-116157000	Enhancers	Fetal Muscle Leg	muscle
5	chr10:116151600-116158400	Enhancers	GM12878-XiMat	blood
6	chr10:116151800-116162600	Weak transcription	Lung	lung
7	chr10:116152800-116156600	Enhancers	Brain Anterior Caudate	brain
8	chr10:116152800-116158800	Enhancers	Rectal Smooth Muscle	rectum
9	chr10:116153200-116157000	Enhancers	Brain Substantia Nigra	brain
10	chr10:116153200-116162600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr10:116153600-116157400	Weak transcription	Fetal Kidney	kidney
12	chr10:116153800-116157200	Weak transcription	A549	lung
13	chr10:116154000-116156200	Weak transcription	Fetal Lung	lung
14	chr10:116154000-116156600	Weak transcription	Right Atrium	heart
15	chr10:116154000-116159200	Enhancers	Spleen	Spleen
16	chr10:116154200-116156600	Weak transcription	Ovary	ovary
17	chr10:116154200-116161200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr10:116154600-116156200	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr10:116154600-116157200	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr10:116154600-116157600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr10:116154800-116156600	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr10:116154800-116157000	Weak transcription	Fetal Thymus	thymus
23	chr10:116154800-116157400	Weak transcription	Esophagus	oesophagus
24	chr10:116155000-116156200	Enhancers	Brain Inferior Temporal Lobe	brain
25	chr10:116155000-116156400	Weak transcription	Fetal Stomach	stomach
26	chr10:116155000-116156400	Weak transcription	Stomach Smooth Muscle	stomach
27	chr10:116155000-116156600	Enhancers	Brain Hippocampus Middle	brain
28	chr10:116155000-116156600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
29	chr10:116155200-116156000	Enhancers	Brain Cingulate Gyrus	brain
30	chr10:116155200-116156200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr10:116155200-116156200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr10:116155200-116157400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr10:116155200-116157600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr10:116155600-116157000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr10:116155600-116157400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr10:116155600-116158200	Genic enhancers	NHEK	skin
37	chr10:116155600-116158400	Weak transcription	Right Ventricle	heart
38	chr10:116155800-116156800	Weak transcription	Fetal Muscle Trunk	muscle
39	chr10:116155800-116157400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr10:116155800-116157400	Weak transcription	Brain Angular Gyrus	brain
41	chr10:116155800-116157600	Weak transcription	Primary hematopoietic stem cells	blood
42	chr10:116155800-116157600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links