Variant report

Variant	rs12664020
Chromosome Location	chr6:38288714-38288715
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:38275306..38278894-chr6:38287022..38290918,3	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11758664	1.00[ASN][1000 genomes]
rs12660215	1.00[CHB][hapmap];0.97[GIH][hapmap];0.90[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12661843	1.00[ASN][1000 genomes]
rs12662422	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13193103	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13197522	1.00[CHB][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13198868	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13206261	1.00[ASN][1000 genomes]
rs13209118	1.00[ASN][1000 genomes]
rs16890541	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs28360643	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36094313	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60814959	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62397020	1.00[ASN][1000 genomes]
rs6907434	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6917308	0.83[EUR][1000 genomes]
rs71571312	1.00[ASN][1000 genomes]
rs7762070	1.00[ASN][1000 genomes]
rs7768902	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7771835	0.83[EUR][1000 genomes]
rs9380755	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv534620	chr6:38049585-38602064	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv885818	chr6:38147745-38436317	Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv885820	chr6:38166511-38468887	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12664020	SRSF3	cis	parietal	SCAN
rs12664020	CNOT8	trans	cerebellum	SCAN
rs12664020	TEAD3	cis	parietal	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38275400-38301200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr6:38278000-38310600	Weak transcription	Gastric	stomach
3	chr6:38278200-38295000	Weak transcription	Lung	lung
4	chr6:38278400-38305400	Weak transcription	Pancreas	Pancrea
5	chr6:38282600-38301400	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr6:38283000-38304000	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr6:38284200-38296000	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr6:38284800-38301200	Weak transcription	Fetal Intestine Small	intestine
9	chr6:38285000-38327800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr6:38286800-38290000	Enhancers	Fetal Muscle Leg	muscle
11	chr6:38286800-38291000	Weak transcription	Psoas Muscle	Psoas
12	chr6:38286800-38295400	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr6:38287200-38289400	Enhancers	Brain Anterior Caudate	brain
14	chr6:38287400-38289200	Enhancers	Brain Substantia Nigra	brain
15	chr6:38287400-38289400	Enhancers	Brain Germinal Matrix	brain
16	chr6:38287400-38289600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr6:38287400-38301200	Weak transcription	Primary B cells from cord blood	blood
18	chr6:38287600-38289400	Flanking Active TSS	GM12878-XiMat	blood
19	chr6:38287600-38290000	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr6:38287600-38301200	Weak transcription	Primary T cells from cord blood	blood
21	chr6:38287800-38289400	Enhancers	Fetal Brain Male	brain
22	chr6:38287800-38290000	Enhancers	Brain Hippocampus Middle	brain
23	chr6:38288000-38289800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr6:38288000-38290000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr6:38288000-38290800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr6:38288000-38290800	Weak transcription	HSMMtube	muscle
27	chr6:38288000-38291000	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr6:38288000-38291000	Weak transcription	Brain Cingulate Gyrus	brain
29	chr6:38288000-38291600	Weak transcription	Fetal Muscle Trunk	muscle
30	chr6:38288000-38292800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr6:38288000-38305600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr6:38288200-38289200	Enhancers	Primary B cells from peripheral blood	blood
33	chr6:38288400-38288800	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
34	chr6:38288400-38289000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
35	chr6:38288400-38289200	Enhancers	Fetal Stomach	stomach
36	chr6:38288400-38290200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr6:38288600-38288800	Enhancers	Right Atrium	heart
38	chr6:38288600-38290000	Enhancers	Fetal Brain Female	brain

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