Variant report

Variant	rs17604946
Chromosome Location	chr5:126760614-126760615
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	chr5:126753682..126756531-chr5:126759834..126762249,2	MCF-7	breast:

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10519936	0.85[CEU][hapmap]
rs10519938	0.85[CEU][hapmap]
rs11950427	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs12233927	0.85[CEU][hapmap]
rs1363388	0.85[CEU][hapmap]
rs17164935	1.00[CEU][hapmap]
rs17165090	0.85[CEU][hapmap]
rs17444885	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17604615	1.00[CEU][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17604665	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17604777	1.00[CHB][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17604819	1.00[CHB][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17604882	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17604889	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17673474	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17673517	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17673685	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17673995	0.94[EUR][1000 genomes]
rs17839690	0.82[EUR][1000 genomes]
rs2068168	1.00[CHB][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2408871	0.85[CEU][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes]
rs3756721	0.85[CEU][hapmap]
rs3812053	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3812054	0.84[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3844184	0.85[CEU][hapmap]
rs3851469	0.85[CEU][hapmap]
rs41298308	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41298312	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57256097	0.92[EUR][1000 genomes]
rs6595768	0.84[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6874752	0.83[EUR][1000 genomes]
rs6881894	0.85[CEU][hapmap]
rs6882034	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6892742	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72788576	0.83[ASN][1000 genomes]
rs72788578	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72788581	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72788599	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72790405	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72790408	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72790410	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72790411	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72790412	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72790417	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72790418	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72790419	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72790422	0.83[EUR][1000 genomes]
rs72790424	0.83[EUR][1000 genomes]
rs72790426	0.83[EUR][1000 genomes]
rs72790428	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72790430	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72790433	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72790438	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72790444	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72790451	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72790460	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72790468	0.95[EUR][1000 genomes]
rs72790470	0.95[EUR][1000 genomes]
rs72790475	0.95[EUR][1000 genomes]
rs72790483	0.94[EUR][1000 genomes]
rs72790485	0.94[EUR][1000 genomes]
rs72790487	0.87[EUR][1000 genomes]
rs73786108	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7718640	0.94[EUR][1000 genomes]
rs7730171	0.91[EUR][1000 genomes]
rs7731380	0.95[EUR][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	nsv1033607	chr5:126385181-127304459	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1019821	chr5:126658200-126934917	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv537894	chr5:126658200-126934917	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1032587	chr5:126691103-126826978	Genic enhancers Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv830478	chr5:126721368-126937408	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:126742800-126762600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr5:126742800-126782000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr5:126742800-126792400	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr5:126743000-126784800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr5:126746400-126760800	Weak transcription	HSMM	muscle
6	chr5:126753400-126761000	Strong transcription	Cortex derived primary cultured neurospheres	brain
7	chr5:126755000-126761800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr5:126755400-126774400	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr5:126755800-126763200	Weak transcription	Brain Angular Gyrus	brain
10	chr5:126756000-126760800	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr5:126756000-126760800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr5:126756000-126768000	Weak transcription	Fetal Brain Male	brain
13	chr5:126756000-126770400	Weak transcription	Fetal Muscle Trunk	muscle
14	chr5:126756800-126760800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr5:126756800-126763600	Weak transcription	Brain Cingulate Gyrus	brain
16	chr5:126757400-126761400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr5:126757400-126761600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr5:126758400-126761000	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr5:126759200-126774000	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr5:126759400-126761000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr5:126759800-126761800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr5:126760200-126760800	Enhancers	Fetal Muscle Leg	muscle
23	chr5:126760200-126761000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr5:126760200-126761200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr5:126760200-126761600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr5:126760200-126761800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr5:126760200-126764400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr5:126760400-126760800	Strong transcription	Brain Anterior Caudate	brain
29	chr5:126760400-126761200	Enhancers	Brain Substantia Nigra	brain
30	chr5:126760400-126761200	Genic enhancers	HSMMtube	muscle
31	chr5:126760400-126761600	Enhancers	Adipose Nuclei	Adipose
32	chr5:126760400-126764200	Enhancers	Fetal Heart	heart
33	chr5:126760400-126778600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr5:126760600-126761200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr5:126760600-126761200	Enhancers	Fetal Intestine Small	intestine
36	chr5:126760600-126764000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr5:126760600-126766200	Enhancers	Brain Hippocampus Middle	brain

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