Variant report

Variant	rs10517269
Chromosome Location	chr4:53709177-53709178
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:53707871..53710353-chr4:53715522..53717667,2	MCF-7	breast:
2	chr4:53707171..53710992-chr4:53726798..53730468,4	MCF-7	breast:
3	chr4:53709061..53711670-chr4:53726343..53729125,3	MCF-7	breast:
4	chr4:53576916..53581689-chr4:53705110..53710230,9	MCF-7	breast:
5	chr4:53708530..53710089-chr4:53712453..53715419,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000212588	Chromatin interaction
ENSG00000264585	Chromatin interaction
ENSG00000128045	Chromatin interaction
ENSG00000226950	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11932601	0.85[CHB][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap]
rs11938159	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11939448	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs17082074	0.80[EUR][1000 genomes]
rs17082084	0.82[LWK][hapmap];0.81[YRI][hapmap]
rs17082087	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17082091	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17630944	0.81[EUR][1000 genomes]
rs17698672	0.84[CEU][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs3811781	0.89[AMR][1000 genomes]
rs58461944	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58577680	0.82[AMR][1000 genomes]
rs59042894	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6554054	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6554057	0.85[CHB][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes]
rs6817433	0.85[CHB][hapmap];0.85[JPT][hapmap];0.91[AMR][1000 genomes]
rs6818178	0.85[CHB][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.89[MEX][hapmap];0.90[YRI][hapmap];0.91[AMR][1000 genomes]
rs6838718	0.85[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6848200	0.89[AMR][1000 genomes]
rs6858566	0.85[JPT][hapmap];0.88[LWK][hapmap];0.85[YRI][hapmap]
rs73814868	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73814886	0.87[AMR][1000 genomes]
rs7655781	0.82[JPT][hapmap];0.91[AMR][1000 genomes]
rs7663419	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7670068	0.85[AMR][1000 genomes]
rs7685816	0.89[AMR][1000 genomes]
rs7688141	0.89[AMR][1000 genomes]
rs7693568	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7699960	0.85[CHB][hapmap];0.85[JPT][hapmap];0.89[MEX][hapmap];0.82[AMR][1000 genomes]
rs881744	0.85[CHB][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.89[MEX][hapmap];0.90[YRI][hapmap];0.91[AMR][1000 genomes]
rs962416	0.84[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594201	chr4:52798624-53732445	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1004889	chr4:53436500-54106281	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv537094	chr4:53436500-54106281	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv1004086	chr4:53698581-53773183	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 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	chr4:53698800-53710600	Enhancers	HUES6 Cell Line	embryonic stem cell
2	chr4:53700200-53710800	Enhancers	ES-I3 Cell Line	embryonic stem cell
3	chr4:53700400-53709600	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr4:53702400-53709200	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr4:53702400-53709800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr4:53704000-53709200	Enhancers	Psoas Muscle	Psoas
7	chr4:53704000-53709200	Enhancers	Skeletal Muscle Female	skeletal muscle
8	chr4:53704000-53709400	Enhancers	Fetal Heart	heart
9	chr4:53704000-53709600	Enhancers	Left Ventricle	heart
10	chr4:53704000-53710000	Enhancers	Fetal Muscle Leg	muscle
11	chr4:53704200-53709800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr4:53704600-53709400	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr4:53705000-53709400	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr4:53705800-53709400	Enhancers	Ovary	ovary
15	chr4:53706000-53710000	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr4:53706600-53709600	Enhancers	Fetal Lung	lung
17	chr4:53706800-53709400	Enhancers	H1 Cell Line	embryonic stem cell
18	chr4:53706800-53709400	Enhancers	Stomach Mucosa	stomach
19	chr4:53706800-53710400	Enhancers	Placenta	Placenta
20	chr4:53707600-53709200	Enhancers	Colon Smooth Muscle	Colon
21	chr4:53707600-53709400	Enhancers	Fetal Stomach	stomach
22	chr4:53707800-53709200	Enhancers	Gastric	stomach
23	chr4:53707800-53709200	Enhancers	Right Atrium	heart
24	chr4:53707800-53709400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr4:53707800-53709600	Enhancers	Right Ventricle	heart
26	chr4:53707800-53709800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr4:53708000-53709200	Enhancers	Fetal Muscle Trunk	muscle
28	chr4:53708000-53709400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr4:53708000-53709400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr4:53708000-53710000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr4:53708200-53709400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr4:53708200-53710000	Enhancers	Fetal Kidney	kidney
33	chr4:53708400-53709200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr4:53708400-53709200	Enhancers	Brain Hippocampus Middle	brain
35	chr4:53708400-53709600	Weak transcription	HSMMtube	muscle
36	chr4:53708400-53710600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr4:53708400-53710600	Enhancers	Primary B cells from peripheral blood	blood
38	chr4:53708400-53714000	Weak transcription	Fetal Intestine Small	intestine
39	chr4:53708400-53719000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr4:53708600-53709200	Enhancers	Stomach Smooth Muscle	stomach
41	chr4:53708600-53710000	Enhancers	Adipose Nuclei	Adipose
42	chr4:53708600-53714000	Weak transcription	Esophagus	oesophagus
43	chr4:53708600-53714000	Weak transcription	Pancreas	Pancrea
44	chr4:53708600-53718000	Weak transcription	Lung	lung
45	chr4:53708800-53710400	Enhancers	Spleen	Spleen
46	chr4:53709000-53709200	Enhancers	Duodenum Mucosa	Duodenum
47	chr4:53709000-53709200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr4:53709000-53709600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr4:53709000-53709600	Enhancers	iPS-15b Cell Line	embryonic stem cell
50	chr4:53709000-53710200	Enhancers	Primary B cells from cord blood	blood

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