Variant report

Variant	rs12670688
Chromosome Location	chr7:106821016-106821017
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:106806204..106812770-chr7:106813358..106822449,17	MCF-7	breast:

Variant related genes	Relation type
ENSG00000105856	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs12112877	0.82[ASN][1000 genomes]
rs12672451	0.95[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13230144	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17153981	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17154040	0.81[ASN][1000 genomes]
rs2107317	1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2237658	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2237659	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2237660	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2237661	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2237662	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2237665	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2283038	0.95[CEU][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2301801	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2395868	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2395869	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34021916	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3801964	0.89[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3801966	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4730220	0.91[ASN][1000 genomes]
rs62482493	0.82[ASN][1000 genomes]
rs62482502	0.81[ASN][1000 genomes]
rs62482503	0.81[ASN][1000 genomes]
rs62483619	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62483623	0.89[ASN][1000 genomes]
rs62483627	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62483629	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62483633	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62483634	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62483640	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62483641	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7777950	0.81[ASN][1000 genomes]
rs7785892	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7788271	0.81[ASN][1000 genomes]
rs7788330	0.81[ASN][1000 genomes]
rs7803151	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs982447	0.81[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	nsv831087	chr7:106673465-106872460	Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv3383027	chr7:106802625-107096474	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12670688	COG5	cis	parietal	SCAN
rs12670688	BCAP29	Cis_1M	lymphoblastoid	RTeQTL
rs12670688	GPR22	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:106810600-106836800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr7:106810800-106826800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:106810800-106828200	Weak transcription	Esophagus	oesophagus
4	chr7:106810800-106836200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr7:106811000-106824200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr7:106811000-106826800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr7:106811000-106826800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr7:106811000-106828800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr7:106811200-106821600	Weak transcription	Thymus	Thymus
10	chr7:106811400-106824800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr7:106811400-106825200	Weak transcription	Lung	lung
12	chr7:106811400-106825800	Weak transcription	NHLF	lung
13	chr7:106812200-106825200	Weak transcription	Aorta	Aorta
14	chr7:106812400-106822600	Weak transcription	Fetal Brain Male	brain
15	chr7:106812400-106826200	Weak transcription	Spleen	Spleen
16	chr7:106814000-106822600	Weak transcription	Fetal Brain Female	brain
17	chr7:106814800-106822400	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr7:106815000-106822600	Weak transcription	Brain Germinal Matrix	brain
19	chr7:106815200-106828200	Weak transcription	Pancreas	Pancrea
20	chr7:106815200-106849400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr7:106815400-106822800	Weak transcription	GM12878-XiMat	blood
22	chr7:106815800-106827800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr7:106816000-106822200	Weak transcription	Fetal Kidney	kidney
24	chr7:106816000-106822400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr7:106816000-106843600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr7:106816800-106823600	Weak transcription	Left Ventricle	heart
27	chr7:106817400-106851400	Strong transcription	Primary B cells from peripheral blood	blood
28	chr7:106817800-106821800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr7:106818600-106821200	Genic enhancers	Primary T cells fromperipheralblood	blood
30	chr7:106819400-106821200	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr7:106819600-106821400	Enhancers	Hela-S3	cervix
32	chr7:106819600-106851800	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr7:106819800-106821200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr7:106819800-106821200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr7:106819800-106821400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr7:106819800-106821400	Enhancers	Duodenum Smooth Muscle	Duodenum
37	chr7:106819800-106821400	Enhancers	HMEC	breast
38	chr7:106819800-106821600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr7:106819800-106821800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr7:106819800-106822000	Enhancers	Fetal Intestine Large	intestine
41	chr7:106819800-106822000	Genic enhancers	Fetal Intestine Small	intestine
42	chr7:106819800-106846600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr7:106819800-106851600	Strong transcription	Dnd41	blood
44	chr7:106820000-106821200	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
45	chr7:106820000-106821200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr7:106820000-106821200	Genic enhancers	K562	blood
47	chr7:106820000-106821400	Enhancers	Muscle Satellite Cultured Cells	--
48	chr7:106820000-106821400	Enhancers	Brain Substantia Nigra	brain
49	chr7:106820000-106821400	Enhancers	Fetal Heart	heart
50	chr7:106820000-106821400	Enhancers	NH-A	brain

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