Variant report

Variant	rs2063239
Chromosome Location	chr12:83274241-83274242
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:83268692..83270482-chr12:83272370..83274630,2	MCF-7	breast:
2	chr12:83260099..83262416-chr12:83272276..83274826,2	K562	blood:
3	chr12:83077297..83078842-chr12:83272817..83275278,2	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10862517	0.80[EUR][1000 genomes]
rs10862518	0.85[YRI][hapmap]
rs10862519	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10862520	0.83[ASW][hapmap];0.83[CEU][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.85[MKK][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11115475	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1508647	0.92[YRI][hapmap]
rs1508648	0.80[LWK][hapmap];0.89[YRI][hapmap]
rs1703088	0.89[YRI][hapmap]
rs1703109	0.85[CHB][hapmap];0.90[JPT][hapmap];0.87[EUR][1000 genomes]
rs1796183	0.80[LWK][hapmap];0.81[YRI][hapmap]
rs6539696	0.85[YRI][hapmap]
rs7296706	0.85[YRI][hapmap]
rs7960995	0.94[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[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:38 , 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	chr12:83271000-83274600	Enhancers	Colon Smooth Muscle	Colon
8	chr12:83272000-83277400	Weak transcription	Brain Germinal Matrix	brain
9	chr12:83272200-83277400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr12:83272800-83274600	Enhancers	Fetal Lung	lung
11	chr12:83273200-83274400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr12:83273200-83274600	Enhancers	Fetal Muscle Leg	muscle
13	chr12:83273200-83275000	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr12:83273400-83274400	Enhancers	Brain Cingulate Gyrus	brain
15	chr12:83273400-83274600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
16	chr12:83273400-83274600	Enhancers	Rectal Smooth Muscle	rectum
17	chr12:83273600-83274400	Enhancers	Fetal Stomach	stomach
18	chr12:83273600-83274600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr12:83273600-83274600	Enhancers	Brain Angular Gyrus	brain
20	chr12:83273600-83274600	Enhancers	Brain Substantia Nigra	brain
21	chr12:83273800-83274600	Enhancers	Fetal Heart	heart
22	chr12:83273800-83275200	Enhancers	Brain Hippocampus Middle	brain
23	chr12:83274000-83274400	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr12:83274000-83274400	Enhancers	Fetal Brain Male	brain
25	chr12:83274000-83274600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr12:83274000-83274800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr12:83274200-83274400	Enhancers	Gastric	stomach
28	chr12:83274200-83274400	Enhancers	Pancreas	Pancrea
29	chr12:83274200-83274400	Enhancers	Sigmoid Colon	Sigmoid Colon
30	chr12:83274200-83274400	Active TSS	Stomach Smooth Muscle	stomach
31	chr12:83274200-83274600	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr12:83274200-83274600	Enhancers	Brain Anterior Caudate	brain
33	chr12:83274200-83274600	Enhancers	Brain Inferior Temporal Lobe	brain
34	chr12:83274200-83274600	Enhancers	Duodenum Mucosa	Duodenum
35	chr12:83274200-83274600	Enhancers	HUVEC	blood vessel
36	chr12:83274200-83274800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr12:83274200-83274800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr12:83274200-83274800	Enhancers	Fetal Brain Female	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links