Variant report

Variant	rs10847456
Chromosome Location	chr12:123164553-123164554
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:123163325..123167706-chr12:123172558..123174898,3	MCF-7	breast:
2	chr12:123143377..123146138-chr12:123164475..123166669,2	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10444445	0.85[CEU][hapmap];0.88[CHB][hapmap];0.81[YRI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10450705	0.81[ASN][1000 genomes]
rs10773429	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10773433	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10773435	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10773436	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10773445	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10773474	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10847452	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10847570	0.88[CHB][hapmap];0.88[MEX][hapmap];0.81[YRI][hapmap]
rs10847574	0.88[CHB][hapmap]
rs11059328	0.81[ASN][1000 genomes]
rs11059333	0.81[ASN][1000 genomes]
rs11059337	0.81[ASN][1000 genomes]
rs11059356	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11059418	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11059504	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11059507	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12231722	0.81[ASN][1000 genomes]
rs1798192	0.81[GIH][hapmap]
rs2088678	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2088682	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2649912	0.86[ASN][1000 genomes]
rs531791	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55776099	0.82[ASN][1000 genomes]
rs61955029	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6489204	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7131791	0.88[CHB][hapmap];0.83[MEX][hapmap]
rs7305589	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7309056	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7958805	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7959072	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7969474	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7970419	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7972971	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10847456	GPR109B	cis	lymphoblastoid	seeQTL

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123161600-123164600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr12:123161600-123164600	Enhancers	Adipose Nuclei	Adipose
3	chr12:123161600-123164600	Enhancers	Placenta	Placenta
4	chr12:123161800-123165000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr12:123162200-123164800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr12:123162600-123164600	Enhancers	HUVEC	blood vessel
7	chr12:123162600-123164800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr12:123162600-123164800	Enhancers	HSMM	muscle
9	chr12:123162600-123164800	Enhancers	NHLF	lung
10	chr12:123162600-123166400	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chr12:123163000-123164600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr12:123163000-123164800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr12:123163000-123164800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr12:123163000-123164800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr12:123163000-123164800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr12:123163000-123164800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr12:123163000-123167600	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr12:123163200-123164600	Enhancers	Hela-S3	cervix
19	chr12:123163200-123164800	Enhancers	Muscle Satellite Cultured Cells	--
20	chr12:123163200-123164800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr12:123163200-123164800	Enhancers	HMEC	breast
22	chr12:123163200-123164800	Enhancers	NH-A	brain
23	chr12:123163200-123164800	Enhancers	NHDF-Ad	bronchial
24	chr12:123163200-123164800	Enhancers	Osteobl	bone
25	chr12:123163200-123166400	Enhancers	Primary B cells from cord blood	blood
26	chr12:123163400-123164600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr12:123163400-123164600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr12:123163400-123164800	Enhancers	HSMMtube	muscle
29	chr12:123163400-123164800	Enhancers	NHEK	skin
30	chr12:123163600-123164800	Enhancers	GM12878-XiMat	blood
31	chr12:123163600-123166200	Enhancers	Monocytes-CD14+_RO01746	blood
32	chr12:123163800-123165000	Enhancers	Primary hematopoietic stem cells	blood
33	chr12:123163800-123165400	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr12:123164200-123164800	Enhancers	A549	lung
35	chr12:123164200-123166000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr12:123164200-123166000	Enhancers	HepG2	liver
37	chr12:123164200-123171600	Weak transcription	Esophagus	oesophagus
38	chr12:123164200-123171800	Weak transcription	Placenta Amnion	Placenta Amnion

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