Variant report

Variant	rs10178717
Chromosome Location	chr2:110452645-110452646
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	chr2:110370667..110373006-chr2:110452355..110454932,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198142	Chromatin interaction
ENSG00000186522	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10185743	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13386685	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13389531	0.94[AFR][1000 genomes]
rs13401439	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13412567	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874777	chr2:109825516-110693317	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1011456	chr2:110290958-110980402	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv535861	chr2:110290958-110980402	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv1009367	chr2:110349178-110863354	Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	esv2762780	chr2:110367969-110462496	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv491837	chr2:110381297-110964737	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv999552	chr2:110396395-110978224	Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
8	nsv428061	chr2:110423940-110714002	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:110439600-110456400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:110441400-110456600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:110442800-110453400	Enhancers	Colon Smooth Muscle	Colon
4	chr2:110446400-110453400	Enhancers	Fetal Intestine Large	intestine
5	chr2:110446400-110453600	Enhancers	Fetal Intestine Small	intestine
6	chr2:110446800-110453000	Enhancers	Fetal Heart	heart
7	chr2:110448600-110456600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr2:110448800-110456400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:110449000-110456600	Weak transcription	Fetal Kidney	kidney
10	chr2:110449200-110453000	Weak transcription	Esophagus	oesophagus
11	chr2:110449200-110453200	Enhancers	Rectal Smooth Muscle	rectum
12	chr2:110449200-110456400	Weak transcription	Left Ventricle	heart
13	chr2:110449400-110453400	Enhancers	HepG2	liver
14	chr2:110450000-110456800	Weak transcription	Right Ventricle	heart
15	chr2:110450200-110453600	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr2:110450200-110456400	Weak transcription	Fetal Muscle Leg	muscle
17	chr2:110450200-110456600	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr2:110450200-110456600	Weak transcription	Right Atrium	heart
19	chr2:110450400-110453600	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr2:110450400-110456600	Weak transcription	Lung	lung
21	chr2:110450400-110456800	Weak transcription	Fetal Muscle Trunk	muscle
22	chr2:110450600-110456400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr2:110450800-110453200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr2:110451000-110458000	Weak transcription	Spleen	Spleen
25	chr2:110451200-110452800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr2:110451200-110456600	Weak transcription	Duodenum Mucosa	Duodenum
27	chr2:110451400-110453000	Enhancers	HUES64 Cell Line	embryonic stem cell
28	chr2:110451400-110453200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr2:110451400-110453200	Enhancers	NHEK	skin
30	chr2:110451600-110453000	Enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr2:110451600-110453000	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr2:110451600-110456800	Weak transcription	Colonic Mucosa	Colon
33	chr2:110451800-110456400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr2:110451800-110456400	Weak transcription	Ovary	ovary
35	chr2:110451800-110456800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr2:110451800-110456800	Weak transcription	Aorta	Aorta
37	chr2:110452000-110452800	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr2:110452000-110453400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr2:110452000-110455400	Weak transcription	Placenta	Placenta
40	chr2:110452000-110456400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr2:110452000-110456600	Weak transcription	Pancreas	Pancrea
42	chr2:110452000-110456600	Weak transcription	NH-A	brain
43	chr2:110452000-110456800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr2:110452200-110456400	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr2:110452200-110456600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr2:110452200-110456600	Weak transcription	Osteobl	bone
47	chr2:110452200-110457200	Weak transcription	Adipose Nuclei	Adipose
48	chr2:110452400-110456200	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr2:110452400-110456400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr2:110452400-110456400	Weak transcription	Stomach Mucosa	stomach

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