Variant report

Variant	rs7623880
Chromosome Location	chr3:110868853-110868854
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:110856185..110858816-chr3:110868086..110870660,2	MCF-7	breast:

Extended variants
information (count: 58 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11717706	0.82[AFR][1000 genomes]
rs11929280	0.85[CEU][hapmap]
rs13060876	0.81[AFR][1000 genomes]
rs13061640	0.81[AFR][1000 genomes]
rs13072462	0.82[AFR][1000 genomes]
rs13093206	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1382075	0.81[AFR][1000 genomes]
rs1477841	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs1477842	1.00[CEU][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs1477843	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs1477846	1.00[CEU][hapmap]
rs1477847	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs1477848	1.00[CEU][hapmap]
rs1477851	0.86[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1547518	0.80[AFR][1000 genomes]
rs2126710	0.81[AFR][1000 genomes]
rs2126713	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs2169643	0.85[CEU][hapmap]
rs2399373	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs2399375	1.00[CEU][hapmap];0.94[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs4682033	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4682034	0.82[AFR][1000 genomes]
rs4682229	1.00[CEU][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs4682230	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs4682231	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs4682234	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs4682238	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55774570	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56668317	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57417964	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6437948	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6437952	0.98[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6437953	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6437955	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs66803420	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs67209183	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6781480	0.81[AFR][1000 genomes]
rs6794645	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7430600	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs7433877	0.85[CEU][hapmap]
rs7610760	1.00[CEU][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7612572	0.82[AFR][1000 genomes]
rs7612667	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs7623847	0.82[AFR][1000 genomes]
rs7632375	0.81[AFR][1000 genomes]
rs7632388	0.81[AFR][1000 genomes]
rs7653595	1.00[CEU][hapmap];0.94[YRI][hapmap];0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs873132	0.85[CEU][hapmap]
rs9288918	0.85[CEU][hapmap]
rs9821335	1.00[CEU][hapmap];0.94[YRI][hapmap]
rs9828899	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs9866028	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs9876350	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003106	chr3:110264476-111105943	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv460821	chr3:110637471-111501097	Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv591275	chr3:110637471-111501097	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	esv1850918	chr3:110685181-110889974	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1008308	chr3:110836281-110885834	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:110816000-110873800	Weak transcription	Left Ventricle	heart
2	chr3:110816000-110893400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:110826800-110884200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr3:110829400-110893400	Weak transcription	HUVEC	blood vessel
5	chr3:110832200-110881800	Weak transcription	Small Intestine	intestine
6	chr3:110832200-110892400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr3:110832400-110911200	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr3:110834000-110891800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr3:110835600-110929600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr3:110836200-110872800	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr3:110838400-110880200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr3:110842600-110911200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr3:110845400-110880000	Weak transcription	Fetal Kidney	kidney
14	chr3:110847000-110873800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr3:110847000-110911400	Weak transcription	Fetal Muscle Leg	muscle
16	chr3:110847200-110873800	Weak transcription	Fetal Intestine Small	intestine
17	chr3:110847200-110874000	Weak transcription	Fetal Stomach	stomach
18	chr3:110848000-110872800	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr3:110848000-110873800	Weak transcription	Fetal Intestine Large	intestine
20	chr3:110848200-110872600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr3:110848200-110891800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr3:110848400-110879800	Weak transcription	Placenta	Placenta
23	chr3:110853000-110872800	Weak transcription	Liver	Liver
24	chr3:110853000-110880000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr3:110853000-110919600	Weak transcription	Fetal Brain Male	brain
26	chr3:110853200-110870000	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr3:110853200-110870000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr3:110853200-110870600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr3:110853200-110873000	Weak transcription	A549	lung
30	chr3:110853200-110873800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr3:110853200-110880200	Weak transcription	Ovary	ovary
32	chr3:110853200-110897000	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr3:110853200-110911000	Weak transcription	NH-A	brain
34	chr3:110853400-110870200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr3:110853400-110879800	Weak transcription	Duodenum Mucosa	Duodenum
36	chr3:110853800-110869200	Weak transcription	HSMM	muscle
37	chr3:110857600-110870600	Weak transcription	NHLF	lung
38	chr3:110857800-110870200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr3:110857800-110892000	Weak transcription	Adipose Nuclei	Adipose
40	chr3:110860800-110875400	Weak transcription	Fetal Heart	heart
41	chr3:110861800-110880200	Weak transcription	HSMMtube	muscle
42	chr3:110862800-110870600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr3:110863000-110875600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr3:110864200-110891800	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr3:110864800-110870000	Weak transcription	NHDF-Ad	bronchial
46	chr3:110865400-110870600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr3:110866800-110873200	Weak transcription	Fetal Lung	lung
48	chr3:110867000-110870200	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr3:110867400-110869000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr3:110867400-110869200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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