Variant report

Variant	rs6442022
Chromosome Location	chr3:46748712-46748713
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:46743022..46745285-chr3:46747232..46748921,2	MCF-7	breast:
2	chr3:46748228..46751973-chr3:46757589..46759527,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000206549	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs4683316	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6803988	0.89[EUR][1000 genomes]
rs6808525	0.83[EUR][1000 genomes]
rs7431776	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9810659	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9861462	0.80[EUR][1000 genomes]
rs9867730	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9868213	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 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	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46743400-46752600	Weak transcription	Left Ventricle	heart
2	chr3:46743400-46758800	Weak transcription	Lung	lung
3	chr3:46743600-46749000	Weak transcription	Psoas Muscle	Psoas
4	chr3:46743600-46750000	Weak transcription	Primary T cells from cord blood	blood
5	chr3:46743600-46752200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr3:46744000-46755800	Weak transcription	Brain Germinal Matrix	brain
7	chr3:46744000-46792200	Weak transcription	Right Atrium	heart
8	chr3:46744400-46750000	Weak transcription	Fetal Brain Male	brain
9	chr3:46744400-46750200	Weak transcription	Fetal Brain Female	brain
10	chr3:46744400-46757400	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr3:46746400-46749600	Enhancers	Placenta Amnion	Placenta Amnion
12	chr3:46746400-46751000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr3:46746600-46748800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
14	chr3:46746600-46748800	Enhancers	Fetal Muscle Leg	muscle
15	chr3:46746600-46750000	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr3:46746800-46748800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr3:46746800-46748800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr3:46746800-46748800	Bivalent Enhancer	Fetal Stomach	stomach
19	chr3:46746800-46749000	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr3:46746800-46749000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
21	chr3:46746800-46749000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr3:46746800-46749200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:46746800-46750600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr3:46747000-46750200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr3:46747000-46750600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr3:46747000-46750800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr3:46747000-46751000	Weak transcription	Ovary	ovary
28	chr3:46747000-46753000	Weak transcription	Right Ventricle	heart
29	chr3:46747000-46755000	Weak transcription	Brain Cingulate Gyrus	brain
30	chr3:46747400-46748800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr3:46747400-46748800	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr3:46747800-46752400	Weak transcription	Fetal Intestine Small	intestine
33	chr3:46748000-46748800	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr3:46748000-46749000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:46748200-46748800	Enhancers	H1 Cell Line	embryonic stem cell
36	chr3:46748200-46749000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr3:46748200-46752000	Weak transcription	HSMMtube	muscle
38	chr3:46748200-46753000	Weak transcription	Spleen	Spleen
39	chr3:46748600-46748800	Enhancers	Fetal Intestine Large	intestine
40	chr3:46748600-46749400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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