Variant report

Variant	rs1703088
Chromosome Location	chr12:83275668-83275669
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	chr12:83275194..83275759-chr14:35873416..35874250,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100906	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10862518	1.00[CEU][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10862520	0.85[YRI][hapmap]
rs11115469	0.96[ASN][1000 genomes]
rs11115495	1.00[CEU][hapmap]
rs1199916	0.96[ASN][1000 genomes]
rs1199917	0.89[ASN][1000 genomes]
rs1199918	0.98[ASN][1000 genomes]
rs1199919	0.93[ASN][1000 genomes]
rs1199920	0.98[ASN][1000 genomes]
rs1199921	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs1208130	0.98[ASN][1000 genomes]
rs12298134	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1508645	0.97[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1508647	0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1508648	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1616906	1.00[ASN][1000 genomes]
rs1703094	0.98[ASN][1000 genomes]
rs1703097	0.96[ASN][1000 genomes]
rs1703098	0.97[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1703102	1.00[CEU][hapmap];0.84[ASN][1000 genomes]
rs1703110	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1796159	1.00[CEU][hapmap];0.98[ASN][1000 genomes]
rs1796181	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1796182	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1796183	1.00[CEU][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1796184	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1796185	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1796190	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1796201	0.96[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs1796202	0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1796203	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1848441	1.00[CEU][hapmap];0.87[YRI][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2063239	0.89[YRI][hapmap]
rs2662077	1.00[CEU][hapmap];0.84[ASN][1000 genomes]
rs2733625	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34592898	0.89[ASN][1000 genomes]
rs6539696	1.00[CEU][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7133985	1.00[CEU][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7134264	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7296706	1.00[CEU][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7299821	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7300604	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7301010	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7304122	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7308048	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7310705	1.00[CEU][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7314923	1.00[CEU][hapmap];0.84[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7960995	0.90[YRI][hapmap]
rs7972978	1.00[ASN][1000 genomes]
rs9788273	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053093	chr12:82645292-83287809	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv541551	chr12:82645292-83287809	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv427917	chr12:82917031-83279712	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Genic enhancers Strong transcription 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	12 gene(s)	inside rSNPs	diseases
4	nsv521849	chr12:83013783-83991479	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv469490	chr12:83089431-83507269	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	nsv559542	chr12:83089431-83507269	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
7	esv2758315	chr12:83101045-83357621	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	esv2759911	chr12:83101045-83357621	Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv832472	chr12:83248283-83419753	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:83242200-83289800	Weak transcription	Stomach Mucosa	stomach
2	chr12:83262200-83278000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr12:83264600-83278000	Weak transcription	Small Intestine	intestine
4	chr12:83264800-83277600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr12:83264800-83277800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:83270000-83277400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr12:83272000-83277400	Weak transcription	Brain Germinal Matrix	brain
8	chr12:83272200-83277400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr12:83274400-83277200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr12:83274400-83277800	Weak transcription	Fetal Brain Male	brain
11	chr12:83274400-83304200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr12:83274600-83277200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:83274600-83277200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr12:83274600-83277200	Weak transcription	Brain Anterior Caudate	brain
15	chr12:83274600-83277200	Weak transcription	Brain Substantia Nigra	brain
16	chr12:83274600-83277400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr12:83274600-83277800	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr12:83274600-83280000	Weak transcription	Colon Smooth Muscle	Colon
19	chr12:83274600-83280400	Weak transcription	Fetal Lung	lung
20	chr12:83274600-83284200	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr12:83274600-83286000	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr12:83274600-83298400	Weak transcription	Brain Angular Gyrus	brain
23	chr12:83274800-83276800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr12:83274800-83282800	Weak transcription	Fetal Brain Female	brain
25	chr12:83275000-83276200	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr12:83275000-83276400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr12:83275200-83277600	Weak transcription	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links