Variant report

Variant	rs17009497
Chromosome Location	chr4:126267997-126267998
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:126265882..126268484-chr4:126269767..126272144,2	MCF-7	breast:

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10212833	0.87[CHB][hapmap];0.80[EUR][1000 genomes]
rs11946554	1.00[YRI][hapmap]
rs12650847	1.00[JPT][hapmap]
rs1509285	0.82[CHB][hapmap];0.80[EUR][1000 genomes]
rs17009521	1.00[MEX][hapmap]
rs17009524	0.82[CHB][hapmap]
rs17009611	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17009615	1.00[JPT][hapmap]
rs17009625	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs17009657	1.00[MEX][hapmap]
rs72673298	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72675308	0.88[ASN][1000 genomes]
rs7666354	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7688616	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs974243	0.86[GIH][hapmap];1.00[JPT][hapmap]
rs992122	0.82[CHB][hapmap]
rs9994504	1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006068	chr4:126103233-126497467	Enhancers ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
2	nsv830051	chr4:126234895-126403426	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:126242800-126279600	Weak transcription	Left Ventricle	heart
2	chr4:126254000-126274000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr4:126265200-126281200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr4:126265400-126268200	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr4:126265800-126268400	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr4:126266000-126268200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr4:126266000-126268200	Enhancers	Brain Substantia Nigra	brain
8	chr4:126266400-126279200	Weak transcription	Fetal Lung	lung
9	chr4:126266800-126268200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr4:126266800-126268200	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr4:126266800-126268200	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr4:126266800-126268200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr4:126267000-126268200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr4:126267000-126268200	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr4:126267000-126268200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr4:126267200-126268200	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr4:126267200-126268200	Active TSS	Brain Angular Gyrus	brain
18	chr4:126267200-126268200	Enhancers	Fetal Kidney	kidney
19	chr4:126267400-126268000	Enhancers	Brain Inferior Temporal Lobe	brain
20	chr4:126267400-126268000	Enhancers	Colon Smooth Muscle	Colon
21	chr4:126267800-126268000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
22	chr4:126267800-126268000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
23	chr4:126267800-126268000	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr4:126267800-126268000	Enhancers	Aorta	Aorta
25	chr4:126267800-126268200	Enhancers	H1 Cell Line	embryonic stem cell
26	chr4:126267800-126268200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr4:126267800-126268200	Flanking Active TSS	Brain Anterior Caudate	brain
28	chr4:126267800-126268200	Enhancers	Brain Cingulate Gyrus	brain
29	chr4:126267800-126268200	Active TSS	Brain Hippocampus Middle	brain

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