Variant report

Variant	rs6427618
Chromosome Location	chr1:161680258-161680259
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10917750	0.87[GIH][hapmap]
rs12038019	0.99[ASN][1000 genomes]
rs12040727	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs12042893	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs12406801	0.87[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2275603	0.92[ASW][hapmap];0.84[CHD][hapmap];0.84[LWK][hapmap];0.80[MEX][hapmap];0.82[MKK][hapmap];0.83[AFR][1000 genomes]
rs6427621	0.99[ASN][1000 genomes]
rs6683580	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2756866	chr1:161344255-161681552	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
2	esv2758972	chr1:161344255-161681552	Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
3	nsv428257	chr1:161406315-161868263	Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	esv33393	chr1:161478681-162080327	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
5	esv1822760	chr1:161480943-161687379	Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
6	nsv464184	chr1:161646807-161885352	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
7	nsv548075	chr1:161646807-161885352	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6427618	PMF1	cis	cerebellum	SCAN
rs6427618	ATF6	cis	parietal	SCAN
rs6427618	DCAF8	cis	parietal	SCAN
rs6427618	FCRLA	cis	multi-tissue	Pritchard
rs6427618	FCRLA	Cis_1M	lymphoblastoid	RTeQTL
rs6427618	FCGR2B	cis	multi-tissue	Pritchard
rs6427618	FCRLM2	cis	multi-tissue	Pritchard

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161675800-161680600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
2	chr1:161676200-161692000	Weak transcription	Spleen	Spleen
3	chr1:161677800-161682400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:161678000-161680400	Weak transcription	HSMMtube	muscle
5	chr1:161679600-161680400	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr1:161679600-161681000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:161679600-161681400	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
8	chr1:161680000-161682000	Genic enhancers	Primary B cells from cord blood	blood
9	chr1:161680000-161682000	Genic enhancers	Primary B cells from peripheral blood	blood
10	chr1:161680000-161682600	Enhancers	K562	blood
11	chr1:161680200-161680400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr1:161680200-161681000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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