Variant report

Variant	rs55650397
Chromosome Location	chr3:46743934-46743935
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:46743022..46745285-chr3:46747232..46748921,2	MCF-7	breast:
2	chr3:46737124..46738860-chr3:46743430..46745835,2	K562	blood:
3	chr3:46734988..46739707-chr3:46741491..46746249,8	K562	blood:

Variant related genes	Relation type
ENSG00000178038	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs12496585	0.82[ASN][1000 genomes]
rs34190208	0.81[ASN][1000 genomes]
rs4076927	0.89[ASN][1000 genomes]
rs56313683	0.80[ASN][1000 genomes]
rs56670151	0.86[ASN][1000 genomes]
rs59191033	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6442020	0.89[ASN][1000 genomes]
rs6776464	0.86[ASN][1000 genomes]
rs6804514	0.91[ASN][1000 genomes]
rs7372799	0.89[ASN][1000 genomes]
rs7373358	0.82[ASN][1000 genomes]
rs73831197	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7426833	0.89[ASN][1000 genomes]
rs7610936	0.87[ASN][1000 genomes]
rs7613489	0.89[ASN][1000 genomes]
rs7633016	0.89[ASN][1000 genomes]
rs7634963	0.81[ASN][1000 genomes]
rs7642448	0.89[ASN][1000 genomes]
rs7642783	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7649029	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7649081	0.88[ASN][1000 genomes]
rs7650366	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007449	chr3:46652343-46986578	Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv536554	chr3:46652343-46986578	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv876739	chr3:46656980-46744966	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv876740	chr3:46656980-46748453	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv876741	chr3:46663372-46763839	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv516623	chr3:46680063-46852679	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	esv2757869	chr3:46680452-46972489	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
8	esv2759147	chr3:46680452-46972489	Genic enhancers Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
9	esv1804680	chr3:46704348-46869911	Bivalent Enhancer Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	nsv876742	chr3:46705369-46763839	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
11	nsv536555	chr3:46706571-46817963	Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
12	nsv536556	chr3:46706571-46849443	Genic enhancers Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
13	nsv536557	chr3:46706571-46853434	Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
14	nsv536558	chr3:46706571-47024756	Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
15	esv1797503	chr3:46708712-46760713	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
16	nsv876743	chr3:46716523-46753577	Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
17	nsv876744	chr3:46716523-46763839	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
18	nsv460525	chr3:46728659-46790397	Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
19	nsv590179	chr3:46728659-46790397	Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
20	esv1847964	chr3:46729757-46753976	Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46740800-46744000	Enhancers	Primary T helper naive cells from peripheral blood	blood
2	chr3:46741200-46744200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
3	chr3:46741200-46744800	Bivalent Enhancer	Fetal Muscle Leg	muscle
4	chr3:46741200-46744800	Enhancers	Skeletal Muscle Female	skeletal muscle
5	chr3:46741400-46744800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
6	chr3:46742600-46744200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr3:46742600-46746400	Weak transcription	Liver	Liver
8	chr3:46742800-46748000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:46743200-46744000	Flanking Active TSS	Fetal Brain Female	brain
10	chr3:46743200-46744000	Enhancers	Right Atrium	heart
11	chr3:46743200-46744000	Enhancers	Right Ventricle	heart
12	chr3:46743200-46744200	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
13	chr3:46743200-46744200	Enhancers	Ovary	ovary
14	chr3:46743400-46744000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
15	chr3:46743400-46744000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr3:46743400-46744000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr3:46743400-46744000	Enhancers	Brain Anterior Caudate	brain
18	chr3:46743400-46744000	Bivalent Enhancer	Fetal Stomach	stomach
19	chr3:46743400-46744400	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr3:46743400-46745200	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr3:46743400-46752600	Weak transcription	Left Ventricle	heart
22	chr3:46743400-46758800	Weak transcription	Lung	lung
23	chr3:46743600-46744000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
24	chr3:46743600-46744200	Enhancers	Brain Hippocampus Middle	brain
25	chr3:46743600-46744400	Enhancers	Fetal Brain Male	brain
26	chr3:46743600-46744800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
27	chr3:46743600-46746400	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr3:46743600-46746800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr3:46743600-46749000	Weak transcription	Psoas Muscle	Psoas
30	chr3:46743600-46750000	Weak transcription	Primary T cells from cord blood	blood
31	chr3:46743600-46752200	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr3:46743800-46744000	Enhancers	Primary T killer memory cells from peripheral blood	blood
33	chr3:46743800-46744000	Enhancers	Brain Germinal Matrix	brain
34	chr3:46743800-46744000	Enhancers	Fetal Heart	heart
35	chr3:46743800-46744200	Enhancers	Primary T helper cells PMA-I stimulated	--
36	chr3:46743800-46744200	Enhancers	Brain Cingulate Gyrus	brain
37	chr3:46743800-46744200	Enhancers	Spleen	Spleen
38	chr3:46743800-46744400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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