Variant report

Variant	rs56077860
Chromosome Location	chr4:48893389-48893390
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:48891196..48894142-chr4:48897336..48899876,3	MCF-7	breast:
2	chr4:48892295..48895717-chr4:48900323..48903334,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145247	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs55909053	1.00[AFR][1000 genomes]
rs55948409	1.00[AFR][1000 genomes]
rs56013049	1.00[AFR][1000 genomes]
rs56196120	1.00[AFR][1000 genomes]
rs56229581	1.00[AFR][1000 genomes]
rs56393041	1.00[AFR][1000 genomes]
rs56784253	1.00[AFR][1000 genomes]
rs58706281	1.00[AFR][1000 genomes]
rs59582819	1.00[AFR][1000 genomes]
rs61152134	1.00[AFR][1000 genomes]
rs6447671	1.00[AFR][1000 genomes]
rs6447672	1.00[AFR][1000 genomes]
rs6447673	1.00[AFR][1000 genomes]
rs6815745	1.00[AFR][1000 genomes]
rs6829709	1.00[AFR][1000 genomes]
rs6842198	1.00[AFR][1000 genomes]
rs6842954	1.00[AFR][1000 genomes]
rs6844156	1.00[AFR][1000 genomes]
rs6849135	1.00[AFR][1000 genomes]
rs6850227	1.00[AFR][1000 genomes]
rs6850983	1.00[AFR][1000 genomes]
rs6857526	1.00[AFR][1000 genomes]
rs6857571	1.00[AFR][1000 genomes]
rs73815328	1.00[AFR][1000 genomes]
rs73815329	1.00[AFR][1000 genomes]
rs73815333	1.00[AFR][1000 genomes]
rs73815337	1.00[AFR][1000 genomes]
rs73815371	1.00[AFR][1000 genomes]
rs73815373	1.00[AFR][1000 genomes]
rs73815393	1.00[AFR][1000 genomes]
rs73815397	1.00[AFR][1000 genomes]
rs73815399	1.00[AFR][1000 genomes]
rs73817712	1.00[AFR][1000 genomes]
rs73817713	1.00[AFR][1000 genomes]
rs73817714	1.00[AFR][1000 genomes]
rs73817715	0.83[AFR][1000 genomes]
rs73817717	1.00[AFR][1000 genomes]
rs73817719	1.00[AFR][1000 genomes]
rs73817721	1.00[AFR][1000 genomes]
rs73817723	1.00[AFR][1000 genomes]
rs73817726	1.00[AFR][1000 genomes]
rs73817729	1.00[AFR][1000 genomes]
rs73817741	1.00[AFR][1000 genomes]
rs73817742	1.00[AFR][1000 genomes]
rs7658876	1.00[AFR][1000 genomes]
rs7674901	1.00[AFR][1000 genomes]
rs7676916	1.00[AFR][1000 genomes]
rs7682222	1.00[AFR][1000 genomes]
rs7684655	1.00[AFR][1000 genomes]
rs7695125	1.00[AFR][1000 genomes]
rs7700082	1.00[AFR][1000 genomes]
rs7700186	1.00[AFR][1000 genomes]
rs9685193	1.00[AFR][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	nsv1002674	chr4:48507608-49032909	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv537087	chr4:48507608-49032909	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1010923	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv537088	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv1013762	chr4:48580484-49032909	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv537089	chr4:48580484-49032909	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv1010381	chr4:48701525-49309842	Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv1003718	chr4:48771947-49083089	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv916809	chr4:48784318-49083302	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
10	nsv1011910	chr4:48784332-49154757	ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	nsv879010	chr4:48794403-49061141	Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
12	nsv1008733	chr4:48827603-48971172	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	nsv427680	chr4:48829607-49660117	ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48860400-48901400	Weak transcription	Brain Hippocampus Middle	brain
2	chr4:48860800-48895000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:48860800-48895000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr4:48874000-48893600	Weak transcription	Pancreas	Pancrea
5	chr4:48877800-48897000	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr4:48879400-48907800	Weak transcription	Right Ventricle	heart
7	chr4:48880600-48894800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr4:48887200-48904200	Weak transcription	Esophagus	oesophagus
9	chr4:48887800-48893400	Weak transcription	HMEC	breast
10	chr4:48887800-48903800	Weak transcription	Placenta	Placenta
11	chr4:48890400-48894800	Weak transcription	Ovary	ovary
12	chr4:48890600-48893400	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr4:48890600-48895000	Weak transcription	HUVEC	blood vessel
14	chr4:48890600-48906200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr4:48890800-48896800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr4:48890800-48898800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr4:48891000-48898800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr4:48891000-48904200	Weak transcription	Spleen	Spleen
19	chr4:48891200-48893400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr4:48891200-48898800	Weak transcription	Stomach Smooth Muscle	stomach
21	chr4:48891200-48902000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr4:48891200-48902800	Weak transcription	Fetal Kidney	kidney
23	chr4:48891200-48907800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr4:48891200-48907800	Weak transcription	Fetal Lung	lung
25	chr4:48891400-48902000	Weak transcription	Colonic Mucosa	Colon
26	chr4:48891400-48907800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr4:48891600-48894800	Weak transcription	Osteobl	bone
28	chr4:48891600-48895000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr4:48891600-48895000	Weak transcription	Gastric	stomach
30	chr4:48891600-48903000	Weak transcription	Hela-S3	cervix
31	chr4:48891800-48893400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr4:48891800-48898400	Weak transcription	Small Intestine	intestine
33	chr4:48891800-48899600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr4:48891800-48901000	Strong transcription	Primary T helper cells PMA-I stimulated	--
35	chr4:48891800-48901800	Strong transcription	Fetal Thymus	thymus
36	chr4:48891800-48904600	Strong transcription	Liver	Liver
37	chr4:48892000-48894800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr4:48892000-48895000	Weak transcription	Fetal Intestine Small	intestine
39	chr4:48892000-48895800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr4:48892000-48899400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr4:48892000-48899400	Strong transcription	Brain Germinal Matrix	brain
42	chr4:48892000-48900200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
43	chr4:48892000-48900800	Strong transcription	Primary T cells from cord blood	blood
44	chr4:48892000-48901200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr4:48892000-48901400	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr4:48892000-48901400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr4:48892000-48901400	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr4:48892000-48902000	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr4:48892000-48905400	Strong transcription	Duodenum Mucosa	Duodenum
50	chr4:48892200-48893800	Weak transcription	H1 Cell Line	embryonic stem cell

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