Variant report

Variant	rs56354230
Chromosome Location	chr10:5906604-5906605
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	chr10:5904346..5907644-chr10:5928919..5931742,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000134461	Chromatin interaction
ENSG00000134452	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11592964	1.00[AFR][1000 genomes]
rs11594153	1.00[AFR][1000 genomes]
rs11595457	1.00[AFR][1000 genomes]
rs11598581	0.90[EUR][1000 genomes]
rs11598865	0.90[EUR][1000 genomes]
rs11813102	0.84[EUR][1000 genomes]
rs17146333	0.87[EUR][1000 genomes]
rs17146580	0.80[EUR][1000 genomes]
rs17146587	0.80[EUR][1000 genomes]
rs17146629	0.80[EUR][1000 genomes]
rs2031230	0.81[EUR][1000 genomes]
rs2137422	1.00[AFR][1000 genomes]
rs2274026	0.83[EUR][1000 genomes]
rs2274028	0.87[EUR][1000 genomes]
rs2274031	0.80[EUR][1000 genomes]
rs2274033	0.80[EUR][1000 genomes]
rs2296136	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs2296137	0.90[EUR][1000 genomes]
rs2296138	0.90[EUR][1000 genomes]
rs34249852	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34455477	0.93[EUR][1000 genomes]
rs3750656	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3750659	0.97[EUR][1000 genomes]
rs41290311	0.90[EUR][1000 genomes]
rs41306916	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4749325	1.00[AFR][1000 genomes]
rs4749407	1.00[AFR][1000 genomes]
rs55718140	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56103646	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56213022	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56296494	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56333805	0.90[EUR][1000 genomes]
rs7893821	0.80[EUR][1000 genomes]
rs7899847	0.90[EUR][1000 genomes]
rs7902223	0.90[EUR][1000 genomes]
rs7904512	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7904712	0.87[EUR][1000 genomes]
rs7912210	0.90[EUR][1000 genomes]
rs7923781	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34147	chr10:5726821-6105717	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats 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	42 gene(s)	inside rSNPs	diseases
2	esv34061	chr10:5726821-6225187	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv1042286	chr10:5795129-6578445	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	nsv831775	chr10:5804335-6000849	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv5654	chr10:5868365-5930634	Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv825229	chr10:5886905-5967697	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv466722	chr10:5893268-5916201	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv549904	chr10:5893268-5916201	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv437655	chr10:5900973-5910361	Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:5894600-5908600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr10:5894600-5908600	Weak transcription	K562	blood
3	chr10:5894600-5916800	Weak transcription	Spleen	Spleen
4	chr10:5896200-5912200	Weak transcription	Fetal Muscle Trunk	muscle
5	chr10:5896400-5918200	Weak transcription	Fetal Lung	lung
6	chr10:5900000-5916600	Weak transcription	Pancreas	Pancrea
7	chr10:5900400-5916200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr10:5900600-5916200	Weak transcription	Stomach Smooth Muscle	stomach
9	chr10:5900800-5910600	Weak transcription	Brain Germinal Matrix	brain
10	chr10:5901000-5916600	Weak transcription	Gastric	stomach
11	chr10:5901200-5918200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr10:5901400-5915200	Weak transcription	Brain Hippocampus Middle	brain
13	chr10:5901600-5912600	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr10:5901600-5915600	Weak transcription	Brain Anterior Caudate	brain
15	chr10:5901800-5910800	Weak transcription	Fetal Brain Female	brain
16	chr10:5902200-5912600	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr10:5902400-5908600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr10:5902400-5918200	Weak transcription	Primary T cells from cord blood	blood
19	chr10:5902600-5910200	Weak transcription	Fetal Muscle Leg	muscle
20	chr10:5902800-5916200	Weak transcription	Fetal Intestine Large	intestine
21	chr10:5902800-5916600	Weak transcription	Brain Substantia Nigra	brain
22	chr10:5902800-5918000	Weak transcription	Lung	lung
23	chr10:5903000-5912400	Weak transcription	Fetal Heart	heart
24	chr10:5903000-5915400	Weak transcription	Duodenum Mucosa	Duodenum
25	chr10:5903400-5911000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr10:5903400-5918200	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr10:5903400-5925000	Weak transcription	Fetal Kidney	kidney
28	chr10:5903600-5916600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr10:5903800-5907200	Strong transcription	Fetal Stomach	stomach
30	chr10:5903800-5913600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr10:5903800-5916000	Weak transcription	NHEK	skin
32	chr10:5903800-5916400	Weak transcription	A549	lung
33	chr10:5903800-5918200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr10:5904400-5916200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr10:5904400-5916200	Weak transcription	Aorta	Aorta
36	chr10:5904600-5915600	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr10:5904600-5916200	Weak transcription	NHDF-Ad	bronchial
38	chr10:5904800-5909800	Weak transcription	Placenta	Placenta
39	chr10:5904800-5911200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr10:5905000-5906800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr10:5905000-5910200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr10:5905000-5910600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr10:5905000-5912000	Weak transcription	Ovary	ovary
44	chr10:5905000-5913400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr10:5905000-5916200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr10:5905000-5916200	Weak transcription	Brain Angular Gyrus	brain
47	chr10:5905200-5908400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr10:5905200-5910000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr10:5905200-5918200	Weak transcription	HepG2	liver
50	chr10:5905400-5908000	Weak transcription	Primary B cells from peripheral blood	blood

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