Variant report

Variant	rs7311274
Chromosome Location	chr12:106207005-106207006
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	chr12:106205255..106208191-chr12:106215389..106217640,2	MCF-7	breast:
2	chr12:106199776..106202110-chr12:106205911..106208055,2	MCF-7	breast:

Extended variants
information (count: 99 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10507199	0.83[ASN][1000 genomes]
rs10732669	0.80[ASW][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[YRI][hapmap];0.85[ASN][1000 genomes]
rs10732670	0.85[ASN][1000 genomes]
rs10735409	0.97[ASN][1000 genomes]
rs10735410	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10735411	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10735412	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10735413	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10746050	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10778440	0.82[ASN][1000 genomes]
rs10778441	0.85[ASN][1000 genomes]
rs10778442	0.85[ASN][1000 genomes]
rs10778446	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10778447	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10778448	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10861505	0.83[ASN][1000 genomes]
rs10861512	0.82[ASN][1000 genomes]
rs10861513	0.80[ASN][1000 genomes]
rs10861514	0.89[ASN][1000 genomes]
rs10861515	0.89[ASN][1000 genomes]
rs10861517	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11112724	0.83[ASN][1000 genomes]
rs11112729	0.85[ASN][1000 genomes]
rs11112730	0.83[ASN][1000 genomes]
rs11112731	0.82[ASN][1000 genomes]
rs11112733	0.85[ASN][1000 genomes]
rs11112736	0.82[ASN][1000 genomes]
rs11112737	0.84[ASN][1000 genomes]
rs11112739	0.89[ASN][1000 genomes]
rs11112747	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11112748	0.91[AFR][1000 genomes]
rs11833529	0.83[ASN][1000 genomes]
rs12305658	0.83[ASN][1000 genomes]
rs12314159	0.93[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs12370329	0.86[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs1421445	0.97[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs1421446	0.97[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs1421447	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1477238	0.96[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs1477239	0.89[ASN][1000 genomes]
rs1477240	0.89[ASN][1000 genomes]
rs1477242	0.89[ASN][1000 genomes]
rs1549103	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2052428	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2111975	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2111976	0.86[ASN][1000 genomes]
rs2374538	0.89[ASN][1000 genomes]
rs2888869	0.83[ASN][1000 genomes]
rs4270016	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4337138	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4430602	0.89[ASN][1000 genomes]
rs4438139	0.85[ASN][1000 genomes]
rs4499093	0.83[ASN][1000 genomes]
rs4509865	0.85[ASN][1000 genomes]
rs4509866	1.00[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.89[YRI][hapmap];0.85[ASN][1000 genomes]
rs4516058	0.89[ASN][1000 genomes]
rs4600310	0.83[ASN][1000 genomes]
rs4609684	0.80[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs4964160	0.88[ASN][1000 genomes]
rs4964161	0.88[ASN][1000 genomes]
rs4964409	0.83[ASN][1000 genomes]
rs4964410	0.85[ASN][1000 genomes]
rs4964411	1.00[CHB][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs4964413	0.84[ASN][1000 genomes]
rs4964414	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4964415	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4964416	0.91[ASN][1000 genomes]
rs6539230	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6539231	0.91[ASN][1000 genomes]
rs7302776	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7307825	0.88[ASN][1000 genomes]
rs7307959	0.86[ASN][1000 genomes]
rs7309925	0.91[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7313258	0.83[ASN][1000 genomes]
rs7313292	0.83[ASN][1000 genomes]
rs750207	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs750208	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7954139	0.89[ASN][1000 genomes]
rs7954308	0.89[ASN][1000 genomes]
rs7954604	1.00[CHB][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7956555	0.83[ASN][1000 genomes]
rs7964548	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7968050	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7968132	1.00[CHB][hapmap];0.85[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7970318	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7979193	0.93[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7979632	0.93[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs878612	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9634186	0.85[ASN][1000 genomes]
rs9634187	0.83[ASN][1000 genomes]
rs9634188	0.83[ASN][1000 genomes]
rs9634189	0.85[ASN][1000 genomes]
rs9634227	1.00[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs9634228	1.00[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs9634229	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039068	chr12:105935786-106211250	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv1047810	chr12:106067049-106246582	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1040261	chr12:106068992-106246582	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv832508	chr12:106198797-106409112	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7311274	NT5DC3	cis	cerebellum	SCAN
rs7311274	CCDC53	cis	parietal	SCAN
rs7311274	PWP1	cis	parietal	SCAN
rs7311274	GAS2L3	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:106192800-106208000	Weak transcription	HSMMtube	muscle
2	chr12:106200200-106212400	Weak transcription	Left Ventricle	heart
3	chr12:106205800-106207400	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr12:106205800-106207400	Enhancers	Aorta	Aorta
5	chr12:106205800-106207600	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr12:106206000-106207800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr12:106206200-106207600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr12:106206200-106208800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr12:106206200-106209000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:106206400-106208200	Weak transcription	Right Ventricle	heart
11	chr12:106206600-106207400	Enhancers	Brain Anterior Caudate	brain
12	chr12:106206600-106209000	Enhancers	Fetal Muscle Leg	muscle
13	chr12:106207000-106207200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr12:106207000-106207400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr12:106207000-106207400	Enhancers	Fetal Stomach	stomach
16	chr12:106207000-106208000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:106207000-106214000	Weak transcription	Right Atrium	heart
18	chr12:106207000-106214400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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