Variant report

Variant	rs6794532
Chromosome Location	chr3:179058225-179058226
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	chr3:178864291..178867045-chr3:179057738..179060531,2	MCF-7	breast:
2	chr3:179058180..179060187-chr3:179061316..179064047,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF639-1	chr3:179058110-179059675	NONHSAT093392
2	lnc-ZNF639-1	chr3:179058110-179059675	ENSG00000260743.1

Variant related genes	Relation type
ENSG00000121879	Chromatin interaction
ENSG00000229102	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1061751	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10937003	0.84[ASN][1000 genomes]
rs11539416	0.84[ASN][1000 genomes]
rs11714246	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11714353	0.81[ASN][1000 genomes]
rs11715130	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11716462	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11720405	0.84[ASN][1000 genomes]
rs12632708	0.85[ASN][1000 genomes]
rs16848314	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3806687	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55916170	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62410442	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62410443	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62410444	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62410445	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73172210	0.83[ASN][1000 genomes]
rs7610174	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7642257	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7644501	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998253	chr3:178622707-179196274	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv536814	chr3:178622707-179196274	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv3354111	chr3:178833305-179156908	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv1002962	chr3:178943753-179224548	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv536815	chr3:178943753-179224548	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv1003021	chr3:178944806-179246179	Enhancers Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	nsv1006584	chr3:178944822-179241429	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv829806	chr3:178952363-179154373	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
9	nsv471116	chr3:178968634-179252263	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
10	nsv592650	chr3:178968634-179252263	Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
11	nsv1010513	chr3:178976107-179196274	Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
12	nsv536816	chr3:178976107-179196274	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
13	nsv1003514	chr3:178990037-179177029	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:179043400-179065200	Weak transcription	Stomach Mucosa	stomach
2	chr3:179048800-179064200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:179049200-179064200	Weak transcription	Fetal Brain Male	brain
4	chr3:179050800-179059200	Weak transcription	Colonic Mucosa	Colon
5	chr3:179051600-179064200	Weak transcription	Right Ventricle	heart
6	chr3:179051800-179064200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr3:179051800-179064200	Weak transcription	Primary T cells from cord blood	blood
8	chr3:179051800-179064200	Weak transcription	Brain Angular Gyrus	brain
9	chr3:179051800-179064200	Weak transcription	Esophagus	oesophagus
10	chr3:179051800-179064200	Weak transcription	Ovary	ovary
11	chr3:179051800-179064200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr3:179051800-179064200	Weak transcription	Thymus	Thymus
13	chr3:179051800-179064200	Weak transcription	NHLF	lung
14	chr3:179051800-179065200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr3:179051800-179065200	Weak transcription	Spleen	Spleen
16	chr3:179052000-179064000	Weak transcription	Fetal Kidney	kidney
17	chr3:179052000-179064200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr3:179052000-179065200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr3:179052200-179064000	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr3:179052200-179064200	Weak transcription	Primary hematopoietic stem cells	blood
21	chr3:179052200-179064200	Weak transcription	Colon Smooth Muscle	Colon
22	chr3:179052200-179064200	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr3:179052200-179065200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr3:179052400-179064200	Weak transcription	Psoas Muscle	Psoas
25	chr3:179052800-179064200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr3:179052800-179065200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr3:179053200-179064000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr3:179053200-179064000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr3:179053200-179064000	Weak transcription	HepG2	liver
30	chr3:179053200-179064200	Weak transcription	Aorta	Aorta
31	chr3:179053200-179064200	Weak transcription	Lung	lung
32	chr3:179053200-179064200	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr3:179053200-179064200	Weak transcription	HSMMtube	muscle
34	chr3:179053200-179064800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr3:179053400-179064200	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr3:179053400-179064200	Weak transcription	Primary B cells from cord blood	blood
37	chr3:179053400-179064200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr3:179053400-179064200	Weak transcription	Duodenum Mucosa	Duodenum
39	chr3:179053600-179064000	Weak transcription	Fetal Lung	lung
40	chr3:179053600-179064000	Weak transcription	Fetal Muscle Trunk	muscle
41	chr3:179053600-179064200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr3:179053600-179064200	Weak transcription	NHEK	skin
43	chr3:179053800-179064200	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr3:179053800-179065200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr3:179053800-179065200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr3:179054000-179064000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr3:179054000-179064200	Weak transcription	Placenta	Placenta
48	chr3:179054000-179064200	Weak transcription	Left Ventricle	heart
49	chr3:179054200-179064000	Weak transcription	GM12878-XiMat	blood
50	chr3:179054400-179059200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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