Variant report

Variant	rs6663978
Chromosome Location	chr1:226797334-226797335
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:226796572..226799349-chr1:227127668..227129647,2	K562	blood:
2	chr1:226796607..226797490-chr1:226821558..226822493,2	K562	blood:
3	chr1:226789700..226792954-chr1:226793236..226797673,6	K562	blood:

Variant related genes	Relation type
ENSG00000163050	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10799362	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916017	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12086463	0.86[CHD][hapmap]
rs3738717	0.82[CHB][hapmap]
rs3738719	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3738720	0.97[ASN][1000 genomes]
rs3820632	0.82[CHB][hapmap];0.87[CHD][hapmap]
rs6664080	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6664299	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6667555	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6697883	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7512486	0.82[CHB][hapmap];0.84[CHD][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	nsv470779	chr1:226778432-226833304	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv873234	chr1:226779449-226859676	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	esv3437833	chr1:226780025-226810577	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv522446	chr1:226785530-226923938	Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226793000-226797600	Weak transcription	Right Atrium	heart
2	chr1:226793000-226797800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr1:226793000-226797800	Weak transcription	Right Ventricle	heart
4	chr1:226793000-226798400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:226794800-226797600	Weak transcription	Fetal Heart	heart
6	chr1:226795800-226797600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr1:226796000-226797800	Enhancers	Fetal Brain Male	brain
8	chr1:226796200-226798600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr1:226796400-226797800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr1:226796400-226798000	Enhancers	Adipose Nuclei	Adipose
11	chr1:226796400-226798600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr1:226796400-226798600	Enhancers	Placenta	Placenta
13	chr1:226796600-226798200	Enhancers	Fetal Muscle Leg	muscle
14	chr1:226796600-226798400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr1:226796800-226798200	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
16	chr1:226796800-226798600	Enhancers	HSMMtube	muscle
17	chr1:226796800-226798800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr1:226796800-226798800	Enhancers	NHDF-Ad	bronchial
19	chr1:226797000-226798200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr1:226797000-226798400	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr1:226797000-226798400	Enhancers	Fetal Thymus	thymus
22	chr1:226797000-226798600	Enhancers	Stomach Smooth Muscle	stomach

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