Variant report

Variant	rs527902
Chromosome Location	chr12:123215410-123215411
allele	A/G
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	CTCF	chr12:123215340-123215490	AG09319	gingival:	n/a	chr12:123215362-123215375 chr12:123215366-123215375
2	CTCF	chr12:123215300-123215450	HMEC	breast:	n/a	chr12:123215362-123215375 chr12:123215366-123215375
3	CTCF	chr12:123215360-123215510	AoAF	blood vessel:	n/a	chr12:123215362-123215375 chr12:123215366-123215375
4	CTCF	chr12:123215300-123215450	AG04450	lung:	n/a	chr12:123215362-123215375 chr12:123215366-123215375
5	CTCF	chr12:123215300-123215450	AG09319	gingival:	n/a	chr12:123215362-123215375 chr12:123215366-123215375
6	GATA3	chr12:123214647-123215547	T-47D	breast:	n/a	chr12:123215528-123215538 chr12:123214949-123214957
7	CTCF	chr12:123215260-123215410	SAEC	small airway:	n/a	chr12:123215362-123215375 chr12:123215366-123215375
8	GATA3	chr12:123214641-123215576	T-47D	breast:	n/a	chr12:123215528-123215538 chr12:123214949-123214957
9	CTCF	chr12:123215280-123215430	HMF	breast:	n/a	chr12:123215362-123215375 chr12:123215366-123215375
10	RAD21	chr12:123215145-123215646	H1-hESC	embryonic stem cell:	n/a	n/a
11	CTCF	chr12:123215300-123215450	Caco-2	colon:	n/a	chr12:123215362-123215375 chr12:123215366-123215375
12	CTCF	chr12:123215320-123215470	HVMF	connective:	n/a	chr12:123215362-123215375 chr12:123215366-123215375
13	CTCF	chr12:123215280-123215430	AG10803	skin:	n/a	chr12:123215362-123215375 chr12:123215366-123215375
14	CTCF	chr12:123215280-123215430	HCPEpiC	choroid plexus:	n/a	chr12:123215362-123215375 chr12:123215366-123215375
15	POLR2A	chr12:123215406-123215431	MCF-7	breast:	n/a	n/a
16	CTCF	chr12:123215260-123215410	HCPEpiC	choroid plexus:	n/a	chr12:123215362-123215375 chr12:123215366-123215375
17	CEBPB	chr12:123215255-123215801	MCF-7	breast:	n/a	chr12:123215700-123215711 chr12:123215702-123215711
18	POLR2A	chr12:123215393-123215466	HepG2	liver:	n/a	n/a
19	CTCF	chr12:123215140-123215430	RPTEC	kidney:	n/a	chr12:123215362-123215375 chr12:123215366-123215375
20	FOXA1	chr12:123215238-123215503	T-47D	breast:	n/a	n/a
21	MYC	chr12:123215361-123215538	HepG2	liver:	n/a	n/a
22	CTCF	chr12:123215320-123215470	RPTEC	kidney:	n/a	chr12:123215362-123215375 chr12:123215366-123215375
23	CTCF	chr12:123215351-123215421	MCF-7	breast:	n/a	chr12:123215362-123215375 chr12:123215366-123215375
24	CTCF	chr12:123215280-123215430	HBMEC	blood vessel:	n/a	chr12:123215362-123215375 chr12:123215366-123215375
25	REST	chr12:123215149-123215562	PFSK-1	brain:	n/a	chr12:123215295-123215308
26	HEY1	chr12:123215153-123215665	HepG2	liver:	n/a	n/a
27	CTCF	chr12:123215340-123215490	MCF-7	breast:	n/a	chr12:123215362-123215375 chr12:123215366-123215375
28	ZNF263	chr12:123215260-123215669	HEK293-T-REx	kidney:	n/a	chr12:123215564-123215585
29	CTCF	chr12:123215300-123215450	HBMEC	blood vessel:	n/a	chr12:123215362-123215375 chr12:123215366-123215375
30	CTCF	chr12:123215260-123215410	A549	lung:	n/a	chr12:123215362-123215375 chr12:123215366-123215375
31	GATA3	chr12:123214623-123215603	MCF-7	breast:	n/a	chr12:123215528-123215538 chr12:123214949-123214957
32	CTCF	chr12:123215320-123215470	HRE	kidney:	n/a	chr12:123215362-123215375 chr12:123215366-123215375
33	CTCF	chr12:123215280-123215430	AoAF	blood vessel:	n/a	chr12:123215362-123215375 chr12:123215366-123215375
34	CTCF	chr12:123215320-123215470	NHLF	lung:	n/a	chr12:123215362-123215375 chr12:123215366-123215375
35	CTCF	chr12:123215300-123215450	HPAF	blood vessel:	n/a	chr12:123215362-123215375 chr12:123215366-123215375
36	CTCF	chr12:123215350-123215430	HepG2	liver:	n/a	chr12:123215362-123215375 chr12:123215366-123215375
37	CTCF	chr12:123215320-123215470	SAEC	small airway:	n/a	chr12:123215362-123215375 chr12:123215366-123215375
38	RAD21	chr12:123215135-123215511	HepG2	liver:	n/a	n/a
39	CTCF	chr12:123215280-123215430	HCFaa	heart:	n/a	chr12:123215362-123215375 chr12:123215366-123215375
40	CTCF	chr12:123215280-123215430	HRE	kidney:	n/a	chr12:123215362-123215375 chr12:123215366-123215375
41	POLR2A	chr12:123215362-123215458	MCF-7	breast:	n/a	n/a
42	CTCF	chr12:123215320-123215470	Caco-2	colon:	n/a	chr12:123215362-123215375 chr12:123215366-123215375

No.	Distal block	Cell Line	Cell type
1	chr12:123212708..123217136-chr12:123232023..123237517,8	MCF-7	breast:
2	chr12:123210591..123212657-chr12:123213454..123215681,5	MCF-7	breast:
3	chr12:123210768..123212595-chr12:123213230..123215441,2	MCF-7	breast:
4	chr12:123213766..123215849-chr12:123233024..123235349,3	MCF-7	breast:
5	chr12:123214031..123216827-chr12:123235538..123237939,3	MCF-7	breast:

Variant related genes	Relation type
HCAR1	TF binding region
ENSG00000270134	TF binding region
ENSG00000139726	Chromatin interaction
ENSG00000270134	Chromatin interaction
ENSG00000256044	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1696348	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2656815	1.00[ASW][hapmap]
rs513567	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];0.83[JPT][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs525017	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7958155	1.00[ASW][hapmap]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs527902	GPR109B	cis	lymphoblastoid	seeQTL

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123208200-123217000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr12:123211800-123216000	Weak transcription	Primary B cells from cord blood	blood
3	chr12:123212400-123216000	Flanking Active TSS	HMEC	breast
4	chr12:123213000-123216000	Active TSS	Breast Myoepithelial Primary Cells	Breast
5	chr12:123213200-123218200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr12:123213400-123216000	Flanking Active TSS	Adipose Nuclei	Adipose
7	chr12:123213800-123215600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr12:123213800-123216600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr12:123214000-123215600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr12:123214000-123215800	Flanking Active TSS	Placenta	Placenta
11	chr12:123214000-123215800	Bivalent/Poised TSS	Fetal Stomach	stomach
12	chr12:123214200-123215600	Active TSS	Gastric	stomach
13	chr12:123214400-123215600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
14	chr12:123214400-123215800	Active TSS	Brain Inferior Temporal Lobe	brain
15	chr12:123214600-123215600	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr12:123214600-123215600	Active TSS	Brain Angular Gyrus	brain
17	chr12:123214600-123215600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr12:123214600-123215800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr12:123214600-123215800	Active TSS	Fetal Kidney	kidney
20	chr12:123214600-123215800	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
21	chr12:123214600-123215800	Enhancers	GM12878-XiMat	blood
22	chr12:123214800-123215600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr12:123214800-123215600	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr12:123214800-123215600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr12:123214800-123215600	Active TSS	Brain Anterior Caudate	brain
26	chr12:123214800-123215600	Active TSS	Brain Cingulate Gyrus	brain
27	chr12:123214800-123215600	Active TSS	NHEK	skin
28	chr12:123214800-123215800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr12:123214800-123215800	Active TSS	Colonic Mucosa	Colon
30	chr12:123214800-123215800	Active TSS	Pancreatic Islets	Pancreatic Islet
31	chr12:123214800-123216600	Enhancers	Primary neutrophils fromperipheralblood	blood
32	chr12:123214800-123218600	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr12:123215000-123215600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr12:123215000-123215600	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr12:123215000-123215600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr12:123215000-123215600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr12:123215000-123215600	Active TSS	Brain Hippocampus Middle	brain
38	chr12:123215000-123215600	Active TSS	Fetal Intestine Small	intestine
39	chr12:123215000-123215600	Active TSS	Ovary	ovary
40	chr12:123215000-123215600	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
41	chr12:123215000-123215600	Active TSS	Stomach Mucosa	stomach
42	chr12:123215000-123215600	Active TSS	NHLF	lung
43	chr12:123215000-123215800	Active TSS	Aorta	Aorta
44	chr12:123215000-123215800	Active TSS	Duodenum Mucosa	Duodenum
45	chr12:123215000-123215800	Active TSS	Right Atrium	heart
46	chr12:123215000-123215800	Active TSS	Skeletal Muscle Female	skeletal muscle
47	chr12:123215000-123216800	Enhancers	Primary T cells from cord blood	blood
48	chr12:123215200-123215600	Weak transcription	Primary hematopoietic stem cells	blood
49	chr12:123215200-123215600	Enhancers	Primary T helper naive cells from peripheral blood	blood
50	chr12:123215200-123215600	Active TSS	Colon Smooth Muscle	Colon

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