Variant report

Variant	rs525017
Chromosome Location	chr12:123215734-123215735
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:61)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr12:123215640-123215790	HRE	kidney:	n/a	n/a
2	CEBPB	chr12:123215255-123215801	MCF-7	breast:	n/a	chr12:123215700-123215711 chr12:123215702-123215711
3	CEBPB	chr12:123215540-123215765	K562	blood:	n/a	chr12:123215700-123215711 chr12:123215702-123215711
4	CEBPB	chr12:123215590-123215802	HepG2	liver:	n/a	chr12:123215700-123215711 chr12:123215702-123215711
5	CEBPB	chr12:123215523-123215854	HepG2	liver:	n/a	chr12:123215700-123215711 chr12:123215702-123215711

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:123215684-123215734	CMK	blood:	n/a
2	chr12:123215684-123215734	HNPCEpiC	eye:	n/a
3	chr12:123215684-123215734	AG09309	skin:	n/a
4	chr12:123215684-123215734	AG04450	lung:	fetal
5	chr12:123215684-123215734	HepG2	liver:	n/a
6	chr12:123215684-123215734	HPAEpiC	pulmonary alveolar:	n/a
7	chr12:123215684-123215734	HAEpiC	amniotic membrane:	n/a
8	chr12:123215684-123215734	MCF10A-Er-Src	breast:	n/a
9	chr12:123215684-123215734	NT2-D1	testis:	n/a
10	chr12:123215684-123215734	HRPEpiC	eye:	n/a
11	chr12:123215684-123215734	HCT-116	colon:	n/a
12	chr12:123215684-123215734	HUVEC	blood vessel:	n/a
13	chr12:123215684-123215734	BJ	skin:	n/a
14	chr12:123215684-123215734	BE2_C	brain:	n/a
15	chr12:123215684-123215734	RPTEC	kidney:	n/a
16	chr12:123215684-123215734	ECC-1	luminal epithelium:	n/a
17	chr12:123215684-123215734	NH-A	brain:	n/a
18	chr12:123215684-123215734	HRCEpiC	kidney:	n/a
19	chr12:123215684-123215734	AG09319	gingival:	n/a
20	chr12:123215684-123215734	GM19239	blood:	n/a
21	chr12:123215684-123215734	AoSMC	blood vessel:	n/a
22	chr12:123215684-123215734	T-47D	breast:	n/a
23	chr12:123215684-123215734	HRE	kidney:	n/a
24	chr12:123215684-123215734	NHDF-neo	bronchial:	n/a
25	chr12:123215684-123215734	Hela-S3	cervix:	n/a
26	chr12:123215684-123215734	U87	brain:	n/a
27	chr12:123215684-123215734	K562	blood:	n/a
28	chr12:123215684-123215734	HMEC	breast:	n/a
29	chr12:123215684-123215734	SK-N-SH_RA	brain:	n/a
30	chr12:123215684-123215734	GM12892	blood:	n/a
31	chr12:123215684-123215734	HL-60	blood:	n/a
32	chr12:123215684-123215734	HEK293	kidney:	embryo
33	chr12:123215684-123215734	PANC-1	pancreas:	n/a
34	chr12:123215684-123215734	GM12878	blood:	n/a
35	chr12:123215684-123215734	AG04449	skin:	fetal
36	chr12:123215684-123215734	HEEpiC	esophagus:	n/a
37	chr12:123215684-123215734	PrEC	prostate:	n/a
38	chr12:123215684-123215734	IMR90	lung:	fetal
39	chr12:123215684-123215734	HCF	heart:	n/a
40	chr12:123215684-123215734	NB4	blood:	n/a
41	chr12:123215684-123215734	HCPEpiC	choroid plexus:	n/a
42	chr12:123215684-123215734	SAEC	small airway:	n/a
43	chr12:123215684-123215734	Hepatocyte	liver:	n/a
44	chr12:123215684-123215734	SK-N-SH	brain:	n/a
45	chr12:123215684-123215734	ProgFib	skin:	n/a
46	chr12:123215684-123215734	HCM	heart:	n/a
47	chr12:123215684-123215734	NHBE	bronchial:	n/a
48	chr12:123215684-123215734	MCF-7	breast:	n/a
49	chr12:123215684-123215734	Caco-2	colon:	n/a
50	chr12:123215684-123215734	LNCaP	prostate:	n/a

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:123212708..123217136-chr12:123232023..123237517,8	MCF-7	breast:
2	chr12:123213766..123215849-chr12:123233024..123235349,3	MCF-7	breast:
3	chr12:123214031..123216827-chr12:123235538..123237939,3	MCF-7	breast:

No data

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

Extended variants
information (count: 6 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1696348	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2656815	1.00[ASW][hapmap]
rs513567	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.83[JPT][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs527902	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]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899571	chr12:123215734-123363562	Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs525017	GPR109B	cis	lymphoblastoid	seeQTL

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

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	chr12:123213800-123216600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr12:123214000-123215800	Flanking Active TSS	Placenta	Placenta
9	chr12:123214000-123215800	Bivalent/Poised TSS	Fetal Stomach	stomach
10	chr12:123214400-123215800	Active TSS	Brain Inferior Temporal Lobe	brain
11	chr12:123214600-123215800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr12:123214600-123215800	Active TSS	Fetal Kidney	kidney
13	chr12:123214600-123215800	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
14	chr12:123214600-123215800	Enhancers	GM12878-XiMat	blood
15	chr12:123214800-123215800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr12:123214800-123215800	Active TSS	Colonic Mucosa	Colon
17	chr12:123214800-123215800	Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr12:123214800-123216600	Enhancers	Primary neutrophils fromperipheralblood	blood
19	chr12:123214800-123218600	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr12:123215000-123215800	Active TSS	Aorta	Aorta
21	chr12:123215000-123215800	Active TSS	Duodenum Mucosa	Duodenum
22	chr12:123215000-123215800	Active TSS	Right Atrium	heart
23	chr12:123215000-123215800	Active TSS	Skeletal Muscle Female	skeletal muscle
24	chr12:123215000-123216800	Enhancers	Primary T cells from cord blood	blood
25	chr12:123215200-123215800	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr12:123215200-123215800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr12:123215200-123215800	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr12:123215200-123215800	Active TSS	Duodenum Smooth Muscle	Duodenum
29	chr12:123215200-123215800	Enhancers	Placenta Amnion	Placenta Amnion
30	chr12:123215200-123216000	Flanking Active TSS	A549	lung
31	chr12:123215200-123216600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr12:123215200-123216600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr12:123215200-123216800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr12:123215400-123215800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr12:123215400-123215800	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
36	chr12:123215400-123217000	Weak transcription	Thymus	Thymus
37	chr12:123215400-123218800	Enhancers	Fetal Thymus	thymus
38	chr12:123215600-123215800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr12:123215600-123215800	Enhancers	Primary hematopoietic stem cells	blood
40	chr12:123215600-123215800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr12:123215600-123215800	Flanking Active TSS	Ovary	ovary
42	chr12:123215600-123215800	Enhancers	Rectal Mucosa Donor 31	rectum
43	chr12:123215600-123216000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr12:123215600-123216000	Flanking Active TSS	HepG2	liver
45	chr12:123215600-123216000	Flanking Active TSS	Osteobl	bone
46	chr12:123215600-123216600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr12:123215600-123216600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr12:123215600-123216600	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr12:123215600-123218200	Enhancers	Primary monocytes fromperipheralblood	blood
50	chr12:123215600-123218600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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