Variant report

Variant	rs7719525
Chromosome Location	chr5:59988727-59988728
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	chr5:59982671..59990838-chr5:59991133..59997951,12	MCF-7	breast:
2	chr5:59986799..59989085-chr5:59989251..59992450,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000035499	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1026418	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1107232	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1107233	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs12658660	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1379111	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1379113	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1460959	1.00[CHB][hapmap]
rs1563516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1563517	1.00[CHB][hapmap]
rs1563518	1.00[CHB][hapmap]
rs1563519	1.00[CHB][hapmap]
rs1563905	1.00[CHB][hapmap]
rs1563906	1.00[CHB][hapmap]
rs1563907	1.00[CHB][hapmap]
rs16878304	1.00[CEU][hapmap];0.95[YRI][hapmap]
rs16878315	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16878354	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1870012	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1870013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1992613	1.00[CHB][hapmap]
rs2045355	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2061254	1.00[CEU][hapmap]
rs2124751	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2124753	0.83[ASN][1000 genomes]
rs2169254	1.00[CHB][hapmap]
rs2305680	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2591635	1.00[CEU][hapmap]
rs2606688	1.00[CEU][hapmap]
rs286150	1.00[CEU][hapmap]
rs286152	1.00[CEU][hapmap]
rs286157	1.00[CEU][hapmap];0.95[YRI][hapmap]
rs2898298	1.00[CHB][hapmap]
rs34414908	0.83[ASN][1000 genomes]
rs34915115	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3857238	1.00[CHB][hapmap]
rs4273559	1.00[CHB][hapmap]
rs61752571	0.85[ASN][1000 genomes]
rs6871928	1.00[CHB][hapmap]
rs6872509	1.00[CEU][hapmap]
rs7702459	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7706896	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7708849	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7712043	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7713586	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7713673	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7716051	1.00[CHB][hapmap]
rs7733069	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs881066	0.82[ASN][1000 genomes]
rs897671	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs897673	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv598288	chr5:59627555-60003460	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	nsv492277	chr5:59905195-60180834	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv462198	chr5:59969015-60116613	Strong transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv598298	chr5:59969015-60116613	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv1023403	chr5:59969534-60079822	Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv4850	chr5:59976186-60039810	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59962600-59990000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr5:59966000-59988800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr5:59969600-59994800	Weak transcription	Fetal Lung	lung
4	chr5:59971000-59993800	Weak transcription	NHLF	lung
5	chr5:59971000-59994000	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr5:59971000-59994200	Weak transcription	NH-A	brain
7	chr5:59974200-59994200	Weak transcription	Duodenum Mucosa	Duodenum
8	chr5:59974400-59993600	Weak transcription	Hela-S3	cervix
9	chr5:59977200-59991000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr5:59977200-59991200	Weak transcription	Pancreas	Pancrea
11	chr5:59977200-59994800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr5:59980200-59995200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr5:59981800-59994200	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr5:59982400-59993600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr5:59982600-59994800	Weak transcription	Fetal Muscle Leg	muscle
16	chr5:59982800-59991000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr5:59982800-59992400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr5:59982800-59993800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr5:59982800-59994800	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr5:59982800-59994800	Weak transcription	Primary hematopoietic stem cells	blood
21	chr5:59983000-59990000	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr5:59983000-59990200	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr5:59983000-59990800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr5:59983000-59991000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr5:59983000-59991000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr5:59983000-59991200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr5:59983000-59992800	Weak transcription	NHEK	skin
28	chr5:59983000-59994000	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr5:59983000-59994000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr5:59983000-59994000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr5:59983000-59994200	Weak transcription	Thymus	Thymus
32	chr5:59983000-59994600	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr5:59983000-59994800	Weak transcription	Fetal Thymus	thymus
34	chr5:59983000-59994800	Weak transcription	HSMM	muscle
35	chr5:59983200-59991000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr5:59983200-59993800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr5:59983200-59993800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr5:59983800-59991000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr5:59984200-59993000	Weak transcription	NHDF-Ad	bronchial
40	chr5:59984400-59991000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr5:59984400-59991200	Weak transcription	Dnd41	blood
42	chr5:59984600-59991000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr5:59984600-59991200	Weak transcription	A549	lung
44	chr5:59984600-59993000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr5:59984600-59994000	Weak transcription	Fetal Heart	heart
46	chr5:59984600-59994800	Weak transcription	Fetal Intestine Small	intestine
47	chr5:59985000-59991000	Weak transcription	K562	blood
48	chr5:59985200-59991200	Weak transcription	Placenta	Placenta
49	chr5:59986800-59992400	Weak transcription	HepG2	liver
50	chr5:59986800-59994000	Weak transcription	Osteobl	bone

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