Variant report

Variant	rs11948332
Chromosome Location	chr5:177753208-177753209
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:177751727..177753386-chr5:177758828..177761752,2	MCF-7	breast:

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs17081072	0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs2162765	0.86[CHB][hapmap];0.88[AMR][1000 genomes]
rs4976759	0.81[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs62389360	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs749424	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7705063	0.88[AMR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948342	chr5:177384542-178168737	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
2	nsv1029398	chr5:177502106-178070654	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	136 gene(s)	inside rSNPs	diseases
3	nsv1019404	chr5:177507080-177859089	Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	126 gene(s)	inside rSNPs	diseases
4	nsv1021981	chr5:177620372-177825272	Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	105 gene(s)	inside rSNPs	diseases
5	nsv537967	chr5:177620372-177825272	Active TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	105 gene(s)	inside rSNPs	diseases
6	nsv1024689	chr5:177638936-177926244	Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	nsv537968	chr5:177638936-177926244	Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv1025291	chr5:177657927-177756215	Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
9	nsv537970	chr5:177657927-177756215	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
10	nsv883203	chr5:177682664-177766183	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS	Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
11	nsv883205	chr5:177684682-177777888	Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	nsv883206	chr5:177684682-177796121	Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	nsv883208	chr5:177692247-177757764	Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS Strong transcription	Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
14	nsv1027165	chr5:177693601-177843314	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
15	nsv984572	chr5:177737015-177763963	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11948332	CENPJ	trans	lymphoblastoid	RTeQTL

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:177739800-177757800	Weak transcription	Gastric	stomach
2	chr5:177747600-177757600	Weak transcription	Right Ventricle	heart
3	chr5:177749600-177761400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
4	chr5:177750200-177753800	Bivalent Enhancer	Fetal Muscle Leg	muscle
5	chr5:177751000-177756000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr5:177751400-177759600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr5:177751600-177754000	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr5:177751800-177756000	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr5:177752000-177755600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr5:177752000-177758200	Weak transcription	Fetal Intestine Large	intestine
11	chr5:177752000-177758800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr5:177752200-177755600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr5:177752400-177754400	Weak transcription	Spleen	Spleen
14	chr5:177752400-177755000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr5:177752600-177753600	Enhancers	Fetal Brain Male	brain
16	chr5:177752600-177753600	Enhancers	Fetal Brain Female	brain
17	chr5:177752600-177754800	Enhancers	Stomach Smooth Muscle	stomach
18	chr5:177752600-177755200	Enhancers	Fetal Lung	lung
19	chr5:177752600-177758000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr5:177752800-177757200	Weak transcription	Brain Angular Gyrus	brain
21	chr5:177753000-177753600	Weak transcription	Fetal Intestine Small	intestine
22	chr5:177753000-177753800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
23	chr5:177753000-177754200	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr5:177753000-177754400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr5:177753000-177757600	Weak transcription	Left Ventricle	heart
26	chr5:177753200-177754000	Enhancers	Fetal Stomach	stomach

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