Variant report

Variant	rs6858566
Chromosome Location	chr4:53705576-53705577
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10517269	0.85[JPT][hapmap];0.88[LWK][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1109696	0.91[ASW][hapmap]
rs11932601	0.84[ASW][hapmap]
rs11938159	0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs11939448	0.85[JPT][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs17082084	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes]
rs17082087	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17082091	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2007959	0.90[ASW][hapmap]
rs58461944	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59042894	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6554054	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6554057	0.90[YRI][hapmap]
rs6818178	0.85[YRI][hapmap]
rs6838718	0.84[ASW][hapmap];0.85[JPT][hapmap];0.85[LWK][hapmap];0.85[YRI][hapmap];0.90[ASN][1000 genomes]
rs6847299	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap]
rs73814868	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7655781	0.82[JPT][hapmap]
rs7663419	0.90[ASN][1000 genomes]
rs7693568	0.88[ASN][1000 genomes]
rs7699960	0.90[YRI][hapmap]
rs881744	0.85[YRI][hapmap]

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	nsv594201	chr4:52798624-53732445	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1004889	chr4:53436500-54106281	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv537094	chr4:53436500-54106281	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv1004086	chr4:53698581-53773183	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:53698800-53710600	Enhancers	HUES6 Cell Line	embryonic stem cell
2	chr4:53700200-53710800	Enhancers	ES-I3 Cell Line	embryonic stem cell
3	chr4:53700400-53709600	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr4:53701000-53706800	Weak transcription	Stomach Mucosa	stomach
5	chr4:53701000-53707000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr4:53701000-53707800	Weak transcription	Aorta	Aorta
7	chr4:53702200-53705800	Enhancers	NHDF-Ad	bronchial
8	chr4:53702400-53707200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr4:53702400-53709200	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr4:53702400-53709800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr4:53702800-53705600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr4:53702800-53705600	Enhancers	HSMM	muscle
13	chr4:53702800-53706200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr4:53703000-53705600	Enhancers	HSMMtube	muscle
15	chr4:53703000-53707400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr4:53703200-53706400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr4:53703200-53708200	Weak transcription	Fetal Kidney	kidney
18	chr4:53703600-53705600	Flanking Active TSS	NHEK	skin
19	chr4:53703600-53707600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr4:53703800-53705600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr4:53703800-53705600	Enhancers	Brain Cingulate Gyrus	brain
22	chr4:53703800-53705600	Enhancers	Brain Substantia Nigra	brain
23	chr4:53703800-53705800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
24	chr4:53703800-53705800	Enhancers	Placenta	Placenta
25	chr4:53703800-53706000	Enhancers	Brain Anterior Caudate	brain
26	chr4:53703800-53707800	Enhancers	iPS-15b Cell Line	embryonic stem cell
27	chr4:53703800-53709000	Enhancers	Skeletal Muscle Male	skeletal muscle
28	chr4:53704000-53705800	Enhancers	Brain Hippocampus Middle	brain
29	chr4:53704000-53706200	Enhancers	Right Ventricle	heart
30	chr4:53704000-53706400	Enhancers	Right Atrium	heart
31	chr4:53704000-53709200	Enhancers	Psoas Muscle	Psoas
32	chr4:53704000-53709200	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr4:53704000-53709400	Enhancers	Fetal Heart	heart
34	chr4:53704000-53709600	Enhancers	Left Ventricle	heart
35	chr4:53704000-53710000	Enhancers	Fetal Muscle Leg	muscle
36	chr4:53704200-53705600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
37	chr4:53704200-53706800	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr4:53704200-53709800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr4:53704400-53705800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr4:53704400-53708200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr4:53704600-53705600	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr4:53704600-53705600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr4:53704600-53705600	Enhancers	NH-A	brain
44	chr4:53704600-53706200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr4:53704600-53706200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr4:53704600-53706200	Enhancers	Brain Angular Gyrus	brain
47	chr4:53704600-53707400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr4:53704600-53709400	Enhancers	Cortex derived primary cultured neurospheres	brain
49	chr4:53704800-53706000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
50	chr4:53704800-53706400	Enhancers	Fetal Brain Female	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links