Variant report

Variant	rs12040409
Chromosome Location	chr1:161678182-161678183
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:161676218-161678545	GM12891	blood:	n/a	n/a
2	POLR2A	chr1:161676459-161678261	GM12892	blood:	n/a	n/a
3	POLR2A	chr1:161676285-161678577	GM12878	blood:	n/a	n/a
4	MTA3	chr1:161675256-161678479	GM12878	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:161677121..161679577-chr1:161693042..161696902,4	MCF-7	breast:
2	chr1:161677692..161679874-chr1:161691714..161694134,2	MCF-7	breast:
3	chr1:161673791..161676241-chr1:161677854..161679843,2	K562	blood:
4	chr1:161667456..161669424-chr1:161676316..161679255,2	MCF-7	breast:
5	chr1:161677606..161679489-chr1:161695482..161697033,2	MCF-7	breast:

No data

Variant related genes	Relation type
FCRLA	TF binding region
ENSG00000199595	Chromatin interaction
ENSG00000162746	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10917740	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12036723	0.87[EUR][1000 genomes]
rs12043179	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12043181	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12044611	0.82[JPT][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12045955	0.82[CHB][hapmap];0.85[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16857520	0.85[JPT][hapmap];1.00[EUR][1000 genomes]
rs16859391	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs16859935	0.85[TSI][hapmap]
rs17405152	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17414989	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs4301614	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61801161	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61801163	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61801180	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	esv2755678	chr1:161463498-161678377	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	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
6	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
7	esv1817508	chr1:161483404-161678548	Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	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
9	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12040409	FCGR2B	cis	lymphoblastoid	seeQTL

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161675400-161678200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr1:161675400-161678400	Enhancers	NHDF-Ad	bronchial
3	chr1:161675800-161680600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr1:161676000-161679800	Flanking Active TSS	Primary B cells from cord blood	blood
5	chr1:161676200-161692000	Weak transcription	Spleen	Spleen
6	chr1:161676600-161678600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr1:161676800-161679600	Active TSS	GM12878-XiMat	blood
8	chr1:161676800-161679800	Weak transcription	Right Atrium	heart
9	chr1:161677000-161679200	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
10	chr1:161677200-161679400	Weak transcription	Brain Hippocampus Middle	brain
11	chr1:161677600-161679400	Weak transcription	K562	blood
12	chr1:161677600-161680000	Flanking Active TSS	Primary B cells from peripheral blood	blood
13	chr1:161677800-161682400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr1:161678000-161680200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr1:161678000-161680400	Weak transcription	HSMMtube	muscle

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