Variant report

Variant	rs282004
Chromosome Location	chr1:91865536-91865537
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:91862177..91865851-chr1:91867476..91870440,3	K562	blood:
2	chr1:91747922..91748906-chr1:91864564..91866357,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000162669	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1034499	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10801849	0.95[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap]
rs10801851	0.87[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap]
rs10923008	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap]
rs12037980	0.90[ASN][1000 genomes]
rs172191	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1822056	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs204304	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];0.87[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs281934	0.84[ASN][1000 genomes]
rs281973	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs282000	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs282003	0.81[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];0.87[TSI][hapmap];0.91[YRI][hapmap]
rs282011	0.96[ASN][1000 genomes]
rs282017	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs282021	0.87[ASN][1000 genomes]
rs282056	0.86[ASN][1000 genomes]
rs282057	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs3893101	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs693299	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs7541566	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9660466	0.92[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	nsv949516	chr1:91644418-92109261	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv1796351	chr1:91722083-91872374	Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv546806	chr1:91780408-91875505	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs282004	HFM1	cis	parietal	SCAN
rs282004	HFM1	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:91853200-91866800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr1:91853200-91869200	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr1:91853200-91869200	Weak transcription	Stomach Smooth Muscle	stomach
4	chr1:91853200-91869400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr1:91853200-91869600	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr1:91857800-91866800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr1:91861600-91869400	Weak transcription	Primary hematopoietic stem cells	blood
8	chr1:91863600-91869400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr1:91863600-91869600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr1:91863800-91865800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr1:91864000-91866800	Weak transcription	Colon Smooth Muscle	Colon
12	chr1:91864200-91869400	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr1:91864200-91869600	Weak transcription	Rectal Smooth Muscle	rectum
14	chr1:91864400-91865800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr1:91864400-91869400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr1:91865000-91869600	Weak transcription	Fetal Muscle Trunk	muscle
17	chr1:91865200-91865600	Enhancers	Psoas Muscle	Psoas
18	chr1:91865200-91869200	Weak transcription	Fetal Kidney	kidney

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