Variant report

Variant	rs61955029
Chromosome Location	chr12:123195800-123195801
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr12:123195738-123196193	HL-60	blood:	n/a	chr12:123195904-123195917 chr12:123195910-123195923 chr12:123195910-123195923 chr12:123195906-123195913 chr12:123195912-123195919
2	SPI1	chr12:123195711-123196157	GM12891	blood:	n/a	chr12:123195904-123195917 chr12:123195910-123195923 chr12:123195910-123195923 chr12:123195906-123195913 chr12:123195912-123195919
3	SPI1	chr12:123195735-123196183	HL-60	blood:	n/a	chr12:123195904-123195917 chr12:123195910-123195923 chr12:123195910-123195923 chr12:123195906-123195913 chr12:123195912-123195919
4	SPI1	chr12:123195732-123196056	GM12891	blood:	n/a	chr12:123195904-123195917 chr12:123195910-123195923 chr12:123195910-123195923 chr12:123195906-123195913 chr12:123195912-123195919
5	SPI1	chr12:123195527-123196209	GM12878	blood:	n/a	chr12:123195904-123195917 chr12:123195910-123195923 chr12:123195910-123195923 chr12:123195906-123195913 chr12:123195912-123195919
6	SPI1	chr12:123195769-123196065	GM12878	blood:	n/a	chr12:123195904-123195917 chr12:123195910-123195923 chr12:123195910-123195923 chr12:123195906-123195913 chr12:123195912-123195919

Variant related genes	Relation type
ENSG00000256249	TF binding region

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10444445	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10773429	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10773433	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10773435	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10773436	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10773445	0.84[AMR][1000 genomes]
rs10773474	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10773515	0.82[ASN][1000 genomes]
rs10773516	0.89[ASN][1000 genomes]
rs10847452	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10847456	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10847570	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10847574	0.89[ASN][1000 genomes]
rs11059356	0.82[AMR][1000 genomes]
rs11059418	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11059504	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11059507	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11059583	0.82[ASN][1000 genomes]
rs2088678	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2088682	0.89[ASN][1000 genomes]
rs2649912	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28675952	0.81[AMR][1000 genomes]
rs35173057	0.81[ASN][1000 genomes]
rs531791	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs55776099	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6489204	0.84[AMR][1000 genomes]
rs6489237	0.89[ASN][1000 genomes]
rs7131790	0.82[ASN][1000 genomes]
rs7131791	0.82[ASN][1000 genomes]
rs7133768	0.82[AMR][1000 genomes]
rs7305589	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7307192	0.82[ASN][1000 genomes]
rs7309056	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7313367	0.82[ASN][1000 genomes]
rs7958805	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7959072	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7969474	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7970419	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7972971	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][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	esv13329	chr12:123178106-123210671	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	n/a
2	nsv973132	chr12:123184783-123201537	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
3	esv8582	chr12:123186451-123200127	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
4	esv3504363	chr12:123186465-123200093	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
5	esv3504374	chr12:123186465-123200093	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
6	esv3493297	chr12:123187437-123200966	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
7	esv3493308	chr12:123187437-123200966	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
8	esv3348872	chr12:123192296-123213461	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs61955029	GPR109B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123174000-123199800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr12:123187800-123198600	Weak transcription	Adipose Nuclei	Adipose
3	chr12:123192600-123199800	Weak transcription	HepG2	liver
4	chr12:123194400-123196000	Enhancers	NHEK	skin
5	chr12:123194800-123195800	Enhancers	HMEC	breast
6	chr12:123195400-123196000	Enhancers	Monocytes-CD14+_RO01746	blood
7	chr12:123195400-123196600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
8	chr12:123195400-123198600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr12:123195400-123202200	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr12:123195600-123196000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr12:123195600-123198800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr12:123195600-123200000	Weak transcription	Placenta	Placenta
13	chr12:123195800-123198800	Weak transcription	HMEC	breast

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