Variant report

Variant	rs10847570
Chromosome Location	chr12:123206691-123206692
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:123205952..123207948-chr12:123213167..123215455,2	K562	blood:
2	chr12:123204711..123206759-chr12:123209537..123212379,2	MCF-7	breast:
3	chr12:123204275..123207099-chr12:123214252..123216398,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000270134	Chromatin interaction
ENSG00000196917	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10444445	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10773515	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10773516	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10847574	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11059504	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11059507	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11059583	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35173057	0.92[ASN][1000 genomes]
rs496911	0.81[GIH][hapmap]
rs55776099	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61955029	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6489237	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7131790	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7131791	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7307192	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7313367	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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	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
rs10847570	GPR109B	cis	lymphoblastoid	seeQTL

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123200800-123207800	Weak transcription	Lung	lung
2	chr12:123201000-123207800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr12:123201200-123214600	Weak transcription	Spleen	Spleen
4	chr12:123201400-123209400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr12:123201400-123210000	Weak transcription	Primary B cells from cord blood	blood
6	chr12:123204200-123208200	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr12:123204200-123208200	Enhancers	Monocytes-CD14+_RO01746	blood
8	chr12:123204400-123208000	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr12:123204600-123207000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr12:123204600-123207200	Enhancers	Fetal Intestine Large	intestine
11	chr12:123204800-123207000	Enhancers	Fetal Intestine Small	intestine
12	chr12:123204800-123207000	Enhancers	HUVEC	blood vessel
13	chr12:123204800-123208200	Enhancers	HepG2	liver
14	chr12:123205200-123206800	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr12:123205200-123207200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr12:123205200-123214600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr12:123205600-123208200	Enhancers	Primary hematopoietic stem cells	blood
18	chr12:123205600-123208400	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr12:123205800-123206800	Weak transcription	Adipose Nuclei	Adipose
20	chr12:123205800-123207000	Enhancers	NHEK	skin
21	chr12:123205800-123207400	Enhancers	HMEC	breast
22	chr12:123205800-123207800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr12:123205800-123207800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr12:123205800-123209000	Weak transcription	Primary B cells from peripheral blood	blood
25	chr12:123205800-123209800	Weak transcription	Hela-S3	cervix
26	chr12:123205800-123210400	Weak transcription	Placenta	Placenta
27	chr12:123205800-123210400	Weak transcription	NH-A	brain
28	chr12:123206000-123207400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr12:123206400-123207000	Enhancers	Fetal Thymus	thymus
30	chr12:123206400-123208000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr12:123206400-123208400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr12:123206600-123206800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
33	chr12:123206600-123206800	Enhancers	Esophagus	oesophagus
34	chr12:123206600-123206800	Enhancers	Right Atrium	heart
35	chr12:123206600-123207000	Flanking Active TSS	GM12878-XiMat	blood
36	chr12:123206600-123207400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links