Variant report

Variant	rs12277584
Chromosome Location	chr11:34770494-34770495
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	chr11:34621214..34622751-chr11:34769844..34772782,2	MCF-7	breast:
2	chr11:34768738..34771170-chr11:34853652..34856105,2	K562	blood:

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10466455	0.81[ASN][1000 genomes]
rs10768093	0.99[ASN][1000 genomes]
rs10768094	0.81[ASN][1000 genomes]
rs10768097	0.81[ASN][1000 genomes]
rs10836290	0.99[ASN][1000 genomes]
rs10836291	0.99[ASN][1000 genomes]
rs10836292	0.99[ASN][1000 genomes]
rs10836294	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10836300	0.80[ASN][1000 genomes]
rs10836302	0.81[ASN][1000 genomes]
rs10836303	0.81[ASN][1000 genomes]
rs10836304	0.81[ASN][1000 genomes]
rs11032835	0.99[ASN][1000 genomes]
rs11032838	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11032839	0.84[ASN][1000 genomes]
rs11032840	0.81[ASN][1000 genomes]
rs11032852	0.81[ASN][1000 genomes]
rs11499809	0.81[ASN][1000 genomes]
rs12418978	0.84[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs12419729	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12420710	0.98[ASN][1000 genomes]
rs12808010	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1396888	0.80[ASN][1000 genomes]
rs1396889	0.80[ASN][1000 genomes]
rs1472975	0.92[ASN][1000 genomes]
rs1509666	0.80[ASN][1000 genomes]
rs1509667	0.81[ASN][1000 genomes]
rs1509668	0.80[ASN][1000 genomes]
rs1605880	0.81[ASN][1000 genomes]
rs67259191	0.90[ASN][1000 genomes]
rs7112043	0.81[ASN][1000 genomes]
rs7124685	0.80[ASN][1000 genomes]
rs7124826	0.80[ASN][1000 genomes]
rs7924717	0.98[ASN][1000 genomes]
rs7927270	0.98[ASN][1000 genomes]
rs7935860	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7937525	0.99[ASN][1000 genomes]
rs7939918	0.84[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs7940805	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7952315	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs906902	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832117	chr11:34639008-34831199	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv1045130	chr11:34641598-34777725	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv1052192	chr11:34641598-34781288	ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv1051492	chr11:34641598-34789331	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
5	nsv1052008	chr11:34641598-34794024	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
6	nsv467788	chr11:34642493-34770494	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
7	nsv553998	chr11:34642493-34770494	Enhancers Strong transcription Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
8	nsv518807	chr11:34642493-34780936	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
9	nsv519718	chr11:34642493-34780936	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
10	nsv467789	chr11:34642493-34780936	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
11	nsv467790	chr11:34642493-34780936	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
12	nsv553999	chr11:34642493-34780936	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
13	nsv554000	chr11:34643780-34780936	Genic enhancers Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
14	nsv869812	chr11:34648088-34810956	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
15	nsv832118	chr11:34743123-34903951	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
16	nsv897214	chr11:34764251-34821948	Weak transcription Bivalent Enhancer Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12277584	RAG2	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:34752800-34770800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr11:34759800-34780000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr11:34760200-34774400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr11:34760200-34776200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr11:34760200-34776800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr11:34760400-34787000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr11:34762200-34776000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr11:34764800-34776200	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr11:34765000-34777000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr11:34765200-34787000	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr11:34767000-34770800	Weak transcription	Pancreas	Pancrea
12	chr11:34768800-34778200	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr11:34769000-34771000	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr11:34769400-34779800	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr11:34769600-34771600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr11:34769800-34771200	Enhancers	Esophagus	oesophagus
17	chr11:34769800-34773400	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr11:34769800-34773600	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr11:34770000-34771000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr11:34770000-34773000	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr11:34770000-34773400	Enhancers	Psoas Muscle	Psoas
22	chr11:34770200-34770800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr11:34770200-34771400	Weak transcription	Adipose Nuclei	Adipose
24	chr11:34770200-34777000	Weak transcription	Placenta	Placenta
25	chr11:34770400-34770800	Weak transcription	Gastric	stomach

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