Variant report

Variant	rs12192827
Chromosome Location	chr6:36642971-36642972
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr6:36642753-36643066	MCF10A-Er-Src	breast:	n/a	n/a
2	STAT3	chr6:36642748-36643056	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr6:36642724-36643071	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr6:36642724-36643126	MCF10A-Er-Src	breast:	n/a	n/a
5	FOS	chr6:36642724-36643079	MCF10A-Er-Src	breast:	n/a	n/a
6	STAT3	chr6:36642723-36643058	MCF10A-Er-Src	breast:	n/a	n/a
7	MYC	chr6:36642713-36643099	MCF10A-Er-Src	breast:	n/a	n/a
8	STAT3	chr6:36642756-36642985	MCF10A-Er-Src	breast:	n/a	n/a
9	JUND	chr6:36642775-36643038	HepG2	liver:	n/a	chr6:36642900-36642911
10	MYC	chr6:36642768-36643071	MCF10A-Er-Src	breast:	n/a	n/a
11	STAT3	chr6:36642748-36643058	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:36562081..36564755-chr6:36642636..36644724,2	K562	blood:
2	chr6:36581224..36597272-chr6:36642199..36659412,120	MCF-7	breast:
3	chr6:36559895..36571260-chr6:36642384..36648914,19	MCF-7	breast:
4	chr6:36581748..36603537-chr6:36641861..36652365,77	MCF-7	breast:

Variant related genes	Relation type
CDKN1A	TF binding region
ENSG00000263894	Chromatin interaction
ENSG00000112081	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1010423	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1010424	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10947618	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10947619	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10947620	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10947621	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10947622	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10947623	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11758192	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12174270	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12192877	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12206430	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12214686	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3829963	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3829965	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4711458	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4711459	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4711460	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4711461	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4711462	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4714002	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4714003	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58714705	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6457934	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6457935	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6931097	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72853320	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7747146	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9349002	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9349005	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9357222	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9394371	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[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	nsv1031191	chr6:36588974-36718015	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv538201	chr6:36588974-36718015	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 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	chr6:36631000-36644000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr6:36635200-36643800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:36635400-36644000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr6:36635400-36645600	Weak transcription	Small Intestine	intestine
5	chr6:36635600-36644000	Weak transcription	Hela-S3	cervix
6	chr6:36636400-36643800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr6:36636400-36643800	Weak transcription	NH-A	brain
8	chr6:36637000-36643800	Weak transcription	Osteobl	bone
9	chr6:36637200-36643600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr6:36637200-36643800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr6:36637200-36643800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr6:36637200-36643800	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr6:36637200-36643800	Weak transcription	HSMM	muscle
14	chr6:36637800-36643400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr6:36637800-36643400	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr6:36637800-36643800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr6:36637800-36643800	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr6:36638800-36644200	Weak transcription	Ovary	ovary
19	chr6:36640000-36643800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr6:36640000-36643800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr6:36640000-36644000	Weak transcription	Duodenum Mucosa	Duodenum
22	chr6:36640200-36643800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr6:36640400-36645600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr6:36640600-36643200	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr6:36640800-36643800	Weak transcription	Fetal Intestine Small	intestine
26	chr6:36641000-36643800	Weak transcription	Fetal Intestine Large	intestine
27	chr6:36641600-36643000	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr6:36641600-36643800	Enhancers	GM12878-XiMat	blood
29	chr6:36641800-36644000	Enhancers	Fetal Muscle Leg	muscle
30	chr6:36642000-36643000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr6:36642000-36643600	Enhancers	HepG2	liver
32	chr6:36642200-36643000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr6:36642200-36644000	Enhancers	HMEC	breast
34	chr6:36642400-36643200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr6:36642400-36643800	Enhancers	NHEK	skin
36	chr6:36642400-36644000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr6:36642400-36646400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr6:36642600-36643800	Enhancers	HSMMtube	muscle
39	chr6:36642600-36644000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr6:36642800-36643600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr6:36642800-36643600	Weak transcription	Stomach Smooth Muscle	stomach
42	chr6:36642800-36643800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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