Variant report

Variant	rs12197784
Chromosome Location	chr6:140284350-140284351
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:139695184..139697325-chr6:140282600..140285421,2	MCF-7	breast:
2	chr6:140283795..140286173-chr6:140291088..140293837,2	MCF-7	breast:
3	chr6:140283635..140285359-chr6:140286373..140288946,2	K562	blood:
4	chr6:140282684..140285359-chr6:140286233..140287873,2	K562	blood:

Variant related genes	Relation type
ENSG00000164442	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1028467	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12202967	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1338692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1547749	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1977739	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2211064	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2328001	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4416686	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4604289	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6570387	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6906538	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7751424	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9495615	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9495620	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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	nsv869066	chr6:139777114-140639695	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
2	nsv1017015	chr6:140084137-140300565	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1019407	chr6:140087307-140304334	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1016532	chr6:140174639-141029988	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:140280000-140286600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:140281600-140284800	Enhancers	Liver	Liver
3	chr6:140282200-140285800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:140282200-140286000	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr6:140282200-140286400	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr6:140282200-140288800	Weak transcription	NHDF-Ad	bronchial
7	chr6:140282800-140285800	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr6:140282800-140285800	Weak transcription	Fetal Kidney	kidney
9	chr6:140283400-140284800	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr6:140283600-140284400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr6:140283600-140284400	Enhancers	Fetal Intestine Small	intestine
12	chr6:140283600-140285000	Enhancers	Colon Smooth Muscle	Colon
13	chr6:140283800-140284400	Enhancers	Placenta	Placenta
14	chr6:140283800-140284400	Enhancers	K562	blood
15	chr6:140283800-140284600	Enhancers	Rectal Smooth Muscle	rectum
16	chr6:140283800-140284600	Enhancers	Right Atrium	heart
17	chr6:140283800-140284800	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr6:140283800-140285000	Enhancers	Fetal Heart	heart
19	chr6:140283800-140286400	Enhancers	Fetal Lung	lung
20	chr6:140284000-140284400	Weak transcription	Stomach Smooth Muscle	stomach
21	chr6:140284000-140284600	Enhancers	Adipose Nuclei	Adipose
22	chr6:140284000-140284600	Enhancers	Spleen	Spleen
23	chr6:140284000-140284800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr6:140284000-140285000	Enhancers	Ovary	ovary
25	chr6:140284000-140285000	Enhancers	NHLF	lung
26	chr6:140284200-140285000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr6:140284200-140286000	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr6:140284200-140287200	Enhancers	Fetal Stomach	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links