Variant report

Variant	rs12129050
Chromosome Location	chr1:114496607-114496608
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	chr1:114469554..114476691-chr1:114493097..114498363,7	MCF-7	breast:
2	chr1:114446008..114448199-chr1:114495493..114497584,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163349	Chromatin interaction
ENSG00000134262	Chromatin interaction
ENSG00000118655	Chromatin interaction
ENSG00000235527	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10108	0.85[ASW][hapmap];0.94[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.97[LWK][hapmap];0.93[MEX][hapmap];0.95[MKK][hapmap];0.85[TSI][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10494162	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10494163	0.82[CEU][hapmap];0.88[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap];0.80[MEX][hapmap];0.82[MKK][hapmap];0.84[ASN][1000 genomes]
rs11102703	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11102706	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11102707	0.85[ASW][hapmap];0.84[CEU][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11102708	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11102709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12060750	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12125546	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12127377	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1217444	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1503832	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1553449	0.92[ASN][1000 genomes]
rs1553450	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17852555	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.85[MKK][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1910485	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1985435	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1985436	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs41302825	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6537800	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6669370	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6674384	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.81[ASN][1000 genomes]
rs7364	0.88[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs7519860	0.94[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7545300	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7546851	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs756493	0.84[ASN][1000 genomes]
rs878129	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]

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	esv2752424	chr1:114189958-114712958	Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs12129050	DCLRE1B	cis	uninvolved skin	skin_eQTL
rs12129050	DCLRE1B	Cis_1M	lymphoblastoid	RTeQTL
rs12129050	PTPN22	cis	parietal	SCAN
rs12129050	DCLRE1B	cis	multi-tissue	Pritchard
rs12129050	DENND2C	cis	cerebellum	SCAN
rs12129050	DCLRE1B	cis	lymphoblastoid	seeQTL
rs12129050	DCLRE1B	cis	lesional skin	skin_eQTL
rs12129050	DCLRE1B	cis	normal skin	skin_eQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114473600-114499200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:114479000-114517600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:114484000-114510400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:114484000-114510400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr1:114484000-114511200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr1:114484200-114497800	Weak transcription	NHDF-Ad	bronchial
7	chr1:114484200-114499400	Weak transcription	Brain Germinal Matrix	brain
8	chr1:114484200-114499600	Weak transcription	HMEC	breast
9	chr1:114484200-114504800	Weak transcription	Esophagus	oesophagus
10	chr1:114484200-114505600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr1:114484400-114510400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:114485000-114500600	Weak transcription	Lung	lung
13	chr1:114485000-114510400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:114486400-114497200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr1:114486400-114499800	Weak transcription	Fetal Brain Male	brain
16	chr1:114486600-114497400	Weak transcription	Fetal Kidney	kidney
17	chr1:114487800-114498800	Weak transcription	Left Ventricle	heart
18	chr1:114487800-114499200	Weak transcription	Ovary	ovary
19	chr1:114488200-114499000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr1:114489600-114499800	Weak transcription	Fetal Brain Female	brain
21	chr1:114489600-114505800	Weak transcription	Gastric	stomach
22	chr1:114489800-114496800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr1:114489800-114497200	Weak transcription	Osteobl	bone
24	chr1:114489800-114510400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:114490000-114496800	Weak transcription	HSMM	muscle
26	chr1:114490000-114496800	Weak transcription	HSMMtube	muscle
27	chr1:114490000-114497200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr1:114490000-114499400	Weak transcription	NHLF	lung
29	chr1:114490000-114500600	Weak transcription	Pancreas	Pancrea
30	chr1:114490000-114505600	Weak transcription	Aorta	Aorta
31	chr1:114490200-114499200	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr1:114490200-114507200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr1:114490200-114510800	Weak transcription	A549	lung
34	chr1:114490400-114497800	Weak transcription	NH-A	brain
35	chr1:114490400-114499200	Weak transcription	Stomach Mucosa	stomach
36	chr1:114490400-114505000	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr1:114490600-114496800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr1:114490600-114497600	Weak transcription	Hela-S3	cervix
39	chr1:114490600-114499200	Weak transcription	Brain Anterior Caudate	brain
40	chr1:114490600-114499400	Weak transcription	Right Ventricle	heart
41	chr1:114490600-114499400	Weak transcription	Small Intestine	intestine
42	chr1:114490600-114512000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr1:114490800-114499200	Weak transcription	Brain Angular Gyrus	brain
44	chr1:114491000-114496800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr1:114491000-114497200	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr1:114491000-114497200	Weak transcription	GM12878-XiMat	blood
47	chr1:114491000-114497400	Weak transcription	Brain Cingulate Gyrus	brain
48	chr1:114491000-114497600	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr1:114491000-114499000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr1:114491000-114499200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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