Variant report

Variant	rs6040569
Chromosome Location	chr20:11334328-11334329
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs11697845	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11698552	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1883968	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1883970	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2103762	0.80[ASN][1000 genomes]
rs2143872	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2207129	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2223861	0.83[ASN][1000 genomes]
rs2327379	0.84[ASN][1000 genomes]
rs2327403	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2327404	0.86[ASN][1000 genomes]
rs28374547	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4347904	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4359714	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4449203	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4473452	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4473453	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4491786	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4564855	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4813054	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4813055	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4813056	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4813985	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4813986	0.83[ASN][1000 genomes]
rs4813987	0.81[ASN][1000 genomes]
rs4813988	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4813989	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4813990	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4813991	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59242255	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6033110	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6033112	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6033119	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6033120	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6040541	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6040563	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6040568	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6040571	0.84[ASN][1000 genomes]
rs6040572	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6040575	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6040576	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6040578	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6078138	0.92[YRI][hapmap];0.83[AFR][1000 genomes]
rs6104739	0.80[AFR][1000 genomes]
rs6104740	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6108922	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6108923	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6108927	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6108929	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6131195	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6131196	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6131197	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6131199	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6131200	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6134204	0.83[ASN][1000 genomes]
rs6134205	0.82[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs6134212	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6134216	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6134217	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6134219	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6134220	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62193969	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs68130714	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs714655	0.81[CEU][hapmap];0.83[CHB][hapmap];0.81[JPT][hapmap]
rs715370	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs715371	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs715372	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs8119263	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs8119401	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs932460	0.84[ASN][1000 genomes]
rs987743	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065969	chr20:10850562-11464172	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv544181	chr20:10850562-11464172	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv585415	chr20:11134907-11383327	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:11330600-11334400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr20:11330800-11336200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr20:11331000-11338400	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr20:11332400-11334800	Weak transcription	HMEC	breast
5	chr20:11332400-11336200	Weak transcription	Psoas Muscle	Psoas
6	chr20:11332400-11337400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr20:11333000-11335800	Weak transcription	Brain Germinal Matrix	brain
8	chr20:11333400-11334400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr20:11333400-11334400	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr20:11333600-11336200	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr20:11333800-11335400	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr20:11334000-11335200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr20:11334200-11335000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr20:11334200-11335200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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