Variant report

Variant	rs1934908
Chromosome Location	chr1:161680868-161680869
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs11576107	0.87[MKK][hapmap]
rs11585450	0.87[EUR][1000 genomes]
rs11746	1.00[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12134087	1.00[ASW][hapmap];0.88[CHB][hapmap];0.95[GIH][hapmap];0.87[MEX][hapmap];0.93[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs12135523	0.88[CHB][hapmap];0.95[GIH][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap]
rs12136407	1.00[ASW][hapmap];0.88[CHB][hapmap];0.95[GIH][hapmap];0.96[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs1847382	0.80[AMR][1000 genomes]
rs1875763	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
8	nsv524449	chr1:161680868-161681780	Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1934908	ATF6	cis	parietal	SCAN
rs1934908	ARHGEF2	cis	parietal	SCAN
rs1934908	DCAF8	cis	parietal	SCAN
rs1934908	FCRLB	cis	parietal	SCAN
rs1934908	CD1E	cis	cerebellum	SCAN
rs1934908	FCRLA	cis	multi-tissue	Pritchard
rs1934908	FCRLA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161676200-161692000	Weak transcription	Spleen	Spleen
2	chr1:161677800-161682400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr1:161679600-161681000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:161679600-161681400	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
5	chr1:161680000-161682000	Genic enhancers	Primary B cells from cord blood	blood
6	chr1:161680000-161682000	Genic enhancers	Primary B cells from peripheral blood	blood
7	chr1:161680000-161682600	Enhancers	K562	blood
8	chr1:161680200-161681000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr1:161680400-161683600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	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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