Variant report

Variant	rs1927200
Chromosome Location	chr13:39980168-39980169
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1185801	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1186156	0.94[EUR][1000 genomes]
rs1186157	0.80[YRI][hapmap]
rs1535778	0.83[CHB][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes]
rs1752056	0.82[CEU][hapmap]
rs2479090	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4941926	0.83[CHB][hapmap];0.95[AFR][1000 genomes]
rs4943661	0.83[EUR][1000 genomes]
rs498769	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs626904	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs671316	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2754118	chr13:39347702-40222644	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1054600	chr13:39801283-40545027	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
3	nsv1036674	chr13:39841482-40008117	Bivalent Enhancer Genic enhancers Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv900008	chr13:39962791-40020267	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:39971200-39980200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr13:39972800-39988600	Weak transcription	Fetal Muscle Leg	muscle
3	chr13:39975800-39981000	Weak transcription	Right Ventricle	heart
4	chr13:39975800-39988400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr13:39975800-39988600	Weak transcription	Right Atrium	heart
6	chr13:39976000-39981000	Weak transcription	Brain Substantia Nigra	brain
7	chr13:39976200-39984000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr13:39976600-39990600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr13:39977000-39980200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr13:39977000-39987800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr13:39977200-39981000	Weak transcription	Left Ventricle	heart
12	chr13:39977200-39983800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr13:39977400-39983600	Weak transcription	Brain Hippocampus Middle	brain
14	chr13:39977600-39982600	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr13:39977800-39984400	Weak transcription	Psoas Muscle	Psoas
16	chr13:39979200-39980200	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr13:39979200-39981800	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr13:39979400-39980200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr13:39979400-39980200	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr13:39979400-39980200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr13:39979400-39980200	Enhancers	Brain Angular Gyrus	brain
22	chr13:39979400-39980200	Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr13:39979400-39980400	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr13:39979400-39980400	Enhancers	Fetal Heart	heart
25	chr13:39979400-39981600	Enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr13:39979400-39983600	Weak transcription	Fetal Brain Male	brain
27	chr13:39979600-39980200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
28	chr13:39979600-39980200	Enhancers	Fetal Stomach	stomach
29	chr13:39979600-39980400	Enhancers	H1 Cell Line	embryonic stem cell
30	chr13:39979600-39980400	Enhancers	Brain Cingulate Gyrus	brain
31	chr13:39979600-39981600	Enhancers	HUES48 Cell Line	embryonic stem cell
32	chr13:39979800-39980200	Enhancers	ES-I3 Cell Line	embryonic stem cell
33	chr13:39979800-39980400	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr13:39980000-39981000	Weak transcription	Ovary	ovary
35	chr13:39980000-39983600	Weak transcription	Brain Anterior Caudate	brain
36	chr13:39980000-39983600	Weak transcription	Fetal Lung	lung
37	chr13:39980000-39983800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr13:39980000-39983800	Weak transcription	NHDF-Ad	bronchial
39	chr13:39980000-39984000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr13:39980000-39984000	Weak transcription	NHLF	lung

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